The Rabbenu Bachya there explains that by counting we separate the good and the bad but together we are all good. People are bad mainly because of gaiva, where they think that everything given to them they deserve. Saying a hundred brachas a day recognizes that everything comes from Hashem as a Matnas Chinom. It says in SA O’CH 98,5 that a person should not be thinking that he davened well and therefore he is deserving to be answered because that creates a scrutiny of his actions being judged in a harsher way.
David Hamelech said to Shaul that Hashem got you to sin by creating the yetzer hara. Therefore, counting through machtzis hashekel unites the Jews, as we need two half shekolim to make one, so it fights the effect of the yetzer hara. No sin is recognized when we are in unity but unity is broken up through gaiva. David Hamelech miscalculated figuring that the Machtzis Hashekel is a temporary foregiveness on the sin of the Eigel and just required for the building of the mishkan but it is required whenever we count the Jews. Also, the machtzis hashekel was even more required as the count was made with no purpose, so the mashchis took over without seeing good or bad but the bad, somewhat, got converted to good by the uttering of hundred brachas everyday recognizing that everything comes from Hashem as stated above making gaiva disappear but without it, gaiva would break up unity and the theme of the machtzis hashekel will not help.
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