I actually broke this system before the upgrade to trixie….
It was low on memory, so I decided to stop service couchdb, and saw that one way or another, x11 got installed. No use of course, but uses RAM, so removed it. It took a bunch of ynh-deps packages along with it (mastodon-ynh-deps, pixelfed-ynh-deps and a few others).
I had intended to reinstall those afterwards, but apt could not find these packages. There was a bunch of automatically installed packages though, which I apt autoremove’d.
Surprise surprise, at least some of these packages were probably part of the *-ynh-deps packages, resulting in all yunohost app upgrade`s breaking.
To continue the migration to trixie, I’ll remove the broken apps…. Sorry for derailing your thread 
Once the migration started, I ran into similar signing problems as you did, compounded by sources.list-files that have been rewritten to a (for me) alien format with file references to mirrors in /usr/… Anyway, stuck for tonight 