Because those are the hardest to count, they have to be individually processed, manually. As a former election olfficial who worked the polls in two states I know how this is done. We used to use electronic voting machines and switched to paper ballots that are scanned by machine. At the end of the election the machine generates a total paper which is publicly posted as well as a copy returned to the Board of Elections. The machine can be plugged into a phone line and its modem can dial the BOE where it uploads the results. All automatic.
The rest of the votes are mail-in votes, absentee votes, or provisional votes. A provisional vote is one where there is a question about a voter. In any case, even if scannable electronically, they have to be opened, checked that the ballot was signed, check the signature, then make sure the inner envelope (to ensure it remains secret) has no identifying marks. If all these checks pass, the ballot is either given to another person (who does not know who it was that voted) to have the machine scan it, or is placed in the pile of ballots to be scanned (and thus counted).
This very careful process protects the right to vote in secret. Those who know who voted cannot know how those people voted; those who know how people voted cannot know who voted on that ballot. This is all done manually, by hand, even if the forms are scanned electronically it's a tedious labor intensive process.