In my experience they will fit but it's very tight. When you screw the cart back together it will bulge a bit but it will still fit just fine into your gba. I personally used a cr2032 as a temporary battery inside my copy of Pokemon Ruby while I was waiting for the 1616 that I ordered to come in.
What kind of Gameboy cart? Classic Gameboy, Gameboy Color or Gameboy Advance? Boktai games natively uses a 2025 battery. I still have some batteries laying around from when I changed mine. I can't say about other games, but I think you can't go wrong with either.