Don't **DELETE** them.
Attend to the settings for purging and compacting.
I like to use a LONG setting of 30 days for bodies (read or unread), and "while available" for headers.
I prefer to compact on demand, as it can be a slow operation.
Another wise move - every week / fortnight, switch view to messages with bodies, go though and save or extract the interesting ones and delete the junk (and delete after save), and if most groups use the default group settings, switch the read/no bodies purge to 1 or 2 days, then do a PURGE ALL.
If you also set to compact when "x%" wasted space, this will probably trigger a compaction as well.
The purge clears old stuff, and the Compact actually recovers the wasted space.
Are you downloading ALL bodies on some groups?
That sounds like a MASSIVE buildup, and very slow to get unless you're running broadband!