My CX has AC. Even after the swap.
You're going to replace the engine anyway... Buy the one with the least rust. They're freakin' 12 year old cars. Neither one should be more than $2000 even if they're mint. Mine was $2000 and needed a new engine.
If they're on dealership lots, cash and carry should allow you to name your price. Don't finance a $2000 car or you'll be paying for something that doesn't run. For the love of God don't spend $3000 on any CX.
Si's are the most stolen civic model (thus, they carry the higher end of the insurance premiums than any other civic model). They're engines are coveted by the turbo crowd. If you want to boost a D16, then get the Si. The CX engine has no potential.