Of course it will. Less capacity, it means that you'll have more cycles per year (for example you might need to charge base model once in a two days, while air once in a day); or you'll keep air at more extreme battery values (for example you might charge base model every day, but you'll charge it from 25% to 80%, while you'll charge air model every day from 5% to 80%).

That doesn't matter, though. Battery replacement on iPhones is very common procedure and you'll need to replace both batteries eventually.

It doesn’t matter because people who buy iPhone Air likely enjoy owning cutting edge experimental products. So when the folding iPhone comes out in a year or two they will probably switch to that. The battery only needs to survive long enough for that.