“And you shall take the silver of atonement from the Children of Israel and include it with [the rest of] the work for the Tent of Meeting, and it shall be for the Children of Israel as a remembrance before G-d to atone for your souls” (Sh’mos 30:16). Although the “silver of atonement” is presented as being an atonement for counting the amount of people in the nation (30:12), necessary to avoid something bad happening because of the process of counting (see Rashi), here it is presented as a long-term atonement, ever-present in the Mishkan. If the purpose of giving a half-shekel was to avoid the negative consequences of being counted (by counting the half-shekalim instead), why did it become a permanent “remembrance” in the Mishkan; wouldn’t the act of counting the coins instead of the people have been enough? Additionally, since the issue of avoiding directly counting people applies whenever a census is taken, why didn’t the coins used for any subsequent “counting” have to become a “remembrance” too? And why is there no mention of coins being used for the census taken shortly after the Mishkan was built (Bamidbar 1:2), or for the census taken shortly before the nation entered the Promised Land (Bamidbar 26:2)? If “when you count the Children of Israel” (30:12) each person who is counted must give a half-shekel for atonement, why didn’t they? And if they did, why weren’t they mentioned?
Another issue this “silver of atonement” raises is that these half-shekalim made up all of the silver that was accounted for and used in the Mishkan (Sh’mos 38:25-28). If all of the silver necessary for the Mishkan came from the mandatory half-shekalim, why was silver included as one of the materials that must be donated willingly (25:2-3)? This question is discussed by numerous commentators (see https://rabbidmk.wordpress.com/2010/02/18/parashas-terumah-5770/), but perhaps we can present another possibility.
Last week (https://rabbidmk.wordpress.com/2016/02/18/parashas-tetzaveh-5776/), I discussed why the incense altar wasn’t commanded until after the section of the commandments for the Mishkan and its vessels, including the priestly garments, was completed. I referenced the approach of Rabbi Moshe Shamah and Rabbi Meir Spiegelman that initially, before the sin of the golden calf, there would not have been an incense altar, but it became necessary because of the sin. Therefore, when the commandments for the Mishkan as it was originally intended were given (during Moshe’s first 40-day period atop Mt. Sinai), the incense altar wasn’t included, but after that section was completed, the Torah tells us about the commandment for the incense altar, which was added during Moshe’s last 40-day period on Mt. Sinai.
Rabbi Shamah further suggests that the commandment to collect the mandatory half-shekalim “for atonement” was given during that last 40-day stay as well, with the “atonement” being for the sin of the golden calf, not for counting people. According to Rabbi Shamah, the “plague” (30:12) that was avoided by giving the half-shekalim was not one that would have otherwise been caused by counting people directly, but a plague associated with the sin of the golden calf (see 32:35). However, the wording of the verse (30:12), that there would not be a plague “when they are counted,” strongly implies that the plague being avoided would have been because of the counting, as if it wasn’t, the words “when they are counted” have no relevance to the timing of the plague. On the other hand, as previously mentioned, if the purpose of the half-shekalim was to avoid the consequences of taking a census, why weren’t they mentioned by the other censuses?
I would therefore suggest that although taking a census by counting people directly is problematic, and can bring a plague (or other disasters), giving half-shekalim is not the only way to avoid such consequences. As long as the people aren’t being counted directly, the problem is avoided. The half-shekalim mandated here were meant as an atonement for the golden calf (as Rabbi Shamah suggests), and were therefore used in the Mishkan as a permanent “remembrance” of this atonement. However, once giving the half-shekalim became necessary, counting them instead of the people accomplished something else as well — it avoided a potential plague that could have resulted from counting the people directly. True, this could have been accomplished in other ways too (by counting slips of paper, or names written on pieces of paper, or taleisim), but since the half-shekalim were being collected anyway, counting them to determine the number of people made the most sense. This was done at the subsequent censuses as well, where the half-shekalim were given for the offerings brought in the Mishkan (see Rashi on 30:15), but because it was not the only way to avoid the consequences of counting people directly, it was not mentioned there.
Since the atonement for the sin of the golden calf was only necessary after the sin had been committed, the mandatory half-shekelim were not part of the original commandment, when the materials to be donated voluntarily were listed (25:3-7). At that point, since the silver needed for the Mishkan would not have been collected through mandatory donations, it would have had to come from voluntary donations. It was only after the “silver of atonement” became necessary that there was no longer a need for any silver to be donated voluntarily.
It should be noted that when Moshe repeated G-d’s commandments to the nation, including the list of materials to be donated voluntarily (35:5-9), silver was still included, even though Moshe certainly didn’t relay this commandment to the nation until after the sin of the golden calf had already been committed, and therefore after all the silver needed for the Mishkan would be collected through the mandatory half-shekalim. Nevertheless, we do not need to fall back on all the other answers given for why silver was included in the original list, as when Moshe repeated the list to the nation he wasn’t listing all the things that needed to be donated voluntarily, but all the things “that G-d [had] commanded” (35:4) to be donated voluntarily, i.e. the original list, and at the time of the original commandment silver still needed to be donated voluntarily. Rather than G-d repeating every detail of the Mishkan again when He told Moshe that the Mishkan project was back on (during the last set of 40 days), He only told him what had changed, i.e. which things were being added (such as the incense altar) and which things should be done differently (such as how the pillars of the doorway were coated, see https://rabbidmk.wordpress.com/2012/03/15/parashas-vayakhel-pekuday-5772/). Those things that remained the same, though, which was most of the Mishkan, didn’t need to be repeated; all that had to be told to Moshe was that the Mishkan that was described to him in detail approximately three months earlier (during his first 40-day stay atop Mt. Sinai) should be built, albeit with the following changes/additions. Since the list of materials needed didn’t change, there was no specific second commandment repeating them. Therefore, when Moshe repeated the original commandment to the nation, he didnt change anything from what G-d had originally told him, and he included everything that G-d had included. True, silver no longer needed to be donated voluntarily, but since Moshe was repeating G-d’s commandment as faithfully as possible, this distinction wasn’t made.
After the sin of the golden calf, it became necessary for each and every adult male to donate a half-shekel as an atonement for it. By counting these half-shekalim, the number of adult males could be determined without counting them directly, thereby avoiding any of the adverse consequences that counting people directly can bring. And because these half-shekalim provided enough silver for the Mishkan, even though before the sin of the golden calf silver would have had to be donated voluntarily, this was no longer the case.