I dunno Hexatron...
Like you say, SOME weapons do get the 99 treatment and others don't. I use another method to keep that from happening as it can become an inconvenience if you give them to Jin or try to sell them off.
My method has been (since trainer 1.2.0) to drop all my weapons and anything I didn't want 99 of, then hit the mega button (numpad 9 so far unless you change it) then reopen the inventory to see the changes, then deactivate the mega item button (that is press it again) THEN pick up all my weapons.
Since I modded the game to give me all the crafting stuff at the beginning when I start a new character, I generally only have to do this once. I suppose if you keep playing the character through several replays you may have to do this again at some time, but it's not that big a deal, and will save you from a possible crash if Jin gets overloaded.