I think it's under the premise that an ammo box is just like an ammo chain: it's designed to use as little extra weight as possible and every shot you fire dismantles part of the ammo chain itself, so there's nothing to reload. If you had the time and equipment you could make a new one or actually reload it, but that'd be out of the scope of this game. So, maybe reloadable ammo boxes isn't such a great idea after all.
In that sense, an ammo box isn't a magazine; rather, it's a clip, which is just like the big ammo chains. As far as I know you can't easily reload a clip like you would a magazine and bulk mods are meant to facilitate bigger magazines.
Personally, I think DoomRL should switch over to magazines. For the most part, clips are WWI old school and not realistic in this setting (the future!). Don't call it a 'box'. Call it a 'magazine', because that's what it's supposed to mimic. You use up a magazine, toss it out, and pop in a new magazine. Otherwise you're limited to manually pumping in rounds. In that case, bulk mods shouldn't apply to all weapons in the same way; rather, something like a pistol which uses a magazine must have magazines and something like a combat shotgun must be manually reloaded as if it were itself a magazine (which it kinda is, but with a trigger and iron sight built into it).