If you feed an unscrapped junk item into the junk jet gun, it only counts as one ammo. But if you scrap it first, and if it contains multiple parts, you get multiple ammo. Let's say some item contains 2 steel, 2 plastic, and 1 cloth. Leave it unscrapped and you only get 1 ammo for Junk Jet. But scrapping it first gives you FIVE. I'm still early in the game and haven't used the Junk Jet gun much, but this could be a very beneficial thing, as it would mean EXPONENTIAL increase of ammo. And the gun is no slouch with 40 damage. FO3 has a similar gun that fires junk items, but of course you can't scrap them to get more items.
The trouble is that scrapping items seems to be a pain. You can't do it in Pip-Boy. You have to drop the items on the ground, go into workshop mode (which means you can only do it in a settlement), and scrap the item one by one. And since scrapped parts go directly to the workshop, you have to retrieve those parts from the workshop, then finally load it to the Junk Jet gun. Hope future mods will alleviate this.