I see your point, but this will also be a behavior that is different from all other inventory items, so it may be potentially confusing to new players. Also, there may be cases when a player has secondary gun that takes Hop-up Booster, but they want to change their primary weapon and use busters on it, which will not work in the auto-apply-to-compatible-gun model. Or maybe players would want to bring them to their teammate (something you can do with any other inventory item) despite having compatible weapons.
The idea itself isn’t bad; I just see complications with implementation.