I feel like they’re just shoehorned in the game. If I had to guess, it was an item that was going to have more special uses that ended up getting scrapped due to time constraints and there being higher priorities, yet the programming its functionality and the bombchu bowling mini game was completed so they didn’t want to waste that effort by keeping them out of the game.
Overall it’s a very niche item with no real required uses except like once in the Spirit Temple and then when you’re playing the mini game. It’s also weird how you can just obtain them from some treasure chests, and even as one of the gold skulltula rewards iirc, but not from enemy drops.
Additionally, it got pretty much the same treatment in Majora’s Mask, and then for some reason they’re a bonus item in the Oracle games where you obtain them by side quests in the linked games, but they’re completely useless there.
It was only in Phantom Hourglass for the DS (maybe also Spirit Tracks but I don’t remember) did they become a major item that had a valid reason to exist, and the touch screen controls where it has you trace the bombchu’s path to lead it where you want it to detonate worked really well for it.
Does anyone else agree that the bombchu’s existence is kind of weird? I also wonder if the upcoming remake will do more with them, but I doubt it.