Here’s an article to read about the history in Colorado, one of the early states to implement it: https://www.coloradoan.com/story/news/2020/10/01/colorado-mail-in-ballot-absentee-voting-how-state-perfected-system/3572176001/

The signatures are checked in an initial step and then the ballots are removed from the signed envelope and grouped with other ballots before being counted - it’s about as anonymous as in person voting.

Ballots aren’t signed, but the envelopes the ballots are in are.