sry, life is getting in the way and i haven’t had much time to look into this yet 
It seems you are correct! After pruning, it doesn’t clean up the bookmarks[1], while it probably should.
For now, one way to work around this, is to add the --keep-threads option to the prune task. That way threads with recent or local interaction will not be deleted. And bookmarks are also considered interaction for this purpose.
[1] https://akkoma.dev/AkkomaGang/akkoma/src/branch/develop/lib/mix/tasks/pleroma/database.ex#L65