It only makes sense. Not everything in the BG universe is magical. Especially for characters who don't use magic at all - how do unlimited arrows make any sense? Limitations are important and valued.
Limitations are valuable yes, but so is reducing unnecessary micromanagement in a game. I'd rather have it this way myself, instead of having to stop what I'm doing and make a side trip to a merchant or a crafting station to make normal arrows after running out. Magic arrows should require that, of course.
As for unlimited normal arrows, I don't think it's too hard to imagine that characters in the game are gathering materials along the way, and making arrows while they're at camp. We just don't see it explicitly. The game thankfully avoids other real-world activities that would just be additional micro, and can be assumed to be a camp activity like repairing damaged armor and weapons.
