Personally I have become paranoid of 'inventory overflow crashes' since that required to restart EE from the beginning two times for me last year ;-)
So I try to delete what I don't use anymore. (My black hole traders do that too for example, real handle deletion ... without me knowing what consequences that might have considering the 'weird nature' of handles ;-)
I remember Raze's posts about this (can't find the most helpful one at the moment); from what I understood and remember the problem can't be solved by deleting handles, since they can't be used a second time (the current limit is 64,000), if the problem you had is the same as this one and I don't mix things up:
http://larian.com/forums/ubbthreads.php?ubb=showflat&Number=580336#Post580336 Anyway: it seems crafting and trading necessarily causes problems at a certain point, depending on the amount of items you deal with.
PS:
If I had known Sniper's work before ... or maybe payed more attention ;-)
Well, I spawn a talking bed-roll or a talking coffin for zombies, so hopefully there are at least SOME differences ;-)
Bed-rolls are an evolutionary universal, so I'm sure Sniper wouldn't blame you for similarities