I have seen my messages.db file grow from 2 MB to over 40 MB in a few weeks.
I have deleted all messages and emptied my trashcan, then vacuumed the messages.db file with the SQLite3 util - nothing changed.
So I inspected the tables and found out that over 200,000 records were still in the rss_guids table!
Deleting those via SQL commanda solved the issue.
I have no clue what the purpose of this table is, but when I delete messages the records in this table have to be deleted as well.