A bit late, but I wanted to say that I had the same issue after upgrading one of my systems to Bookworm, but not on other two systems which are set up fairly similarly, at least one of which I've been upgrading since Woody. Also, on this system where the email folders wouldn't show, the issue was resolved by upgrading to the latest version 1:115.6.0-1~deb12u1, without any other changes made.
Jaap
