Can I use only one of two batteries in iPad Air (5th)?

That's a good question and I'm certain there's a lot of experimenting that can be done here. There is a circuit board built into the battery pack, here are some pictures:

I would assume the charging circuit is designed for a balanced 2-cell design. Whether or not it would work with only one cell is hard to say. The thing to keep in mind here is safety. These iPad batteries pack a lot of punch and the last thing anyone wants is for one these packs to flame-out because it was overcharged. Do the right thing, get a new battery and install it properly.

Ask yourself this, how would you feel if the person next to you in a plane at 30,000 feet had a hacked Li-ion battery in their iPad? If you do this, I know I wouldn't want to be on the same plane as you :>).