The labels are stored in a comma-delimited column in your member table
So you have a column with
-1 is for your 'inbox'.
When you get a message, your labels apply a similar comma-delimited list
-1,0,2 - would be something in Tentacles and Problems, as well as your inbox.
So let's say you delete 'Evangelion'.
It has to go through and do a full renumbering of -all- labels below that, and track it across all received pms with non-inbox labels. And renumber each of them. You probably notice that it takes a second or so. But it's doing a lot of operations in that second or so, and those operations are not particularly clean. When operations are not particularly clean, you get bug infestations.
No, it's not particularly smart. It's actually better than some other forums, but it's still insane. The schema has ten-year old bits left in it, from back when doing a normalized design was simply not feasible.
And people wonder why I'm asking for money so I can build the new software : /