If they're starting to crack due to age then I'd get them replaced, as possibly a repair might not last as well on an older tyre with the rubber perished a bit. I may, of course, be talking s**te, but that'd be my guess.
Mind you, it might be worth getting the punctures repaired if the tyre place can do 2 repairs for a discount as they're on the same tyre, but it could be the case that if the two punctures are quite close together then it's not something they'll want to touch.
Is the spare exactly the correct size, and how much tread does that have left? If it's virtually new, then leave it as a spare, but otherwise, it
*might* be worth getting the punctures repaired (if viable), using that wheel as a spare (being sure to check its pressure regularly - you don't want to be stuck when you need it), then get the tyre on the spare replaced.A few months back I had to replace two tyres on the van that still had a good 4-5mm of tread left, but one had a puncture, and both had been losing pressure (only very gradually, but it's a PITA to have to keep on topping them up to the tune of about 5-10psi/week, when they really should barely be losing any). It's a lesson learned - previously I'd always just made the rears last and last and last, and just replaced the fronts - now I'll be rotating them, so no tyre has to go into forced early retirement due to old age (an oxymoron?).
Peter