it's not a big problem, especially if you still have the other screw. they just hold the nut on the guitar, and keep it from sliding around. the strings do the same thing.
Well that's holding the nut in place, and you probably want a replacement. But, if it's giving no problems and the action isn't out of wack, then you're probably fine.

As far as replacement parts go, these small parts are usually a pain in the arse to find. You should check what the other screw is like, and match up the measurements of it, to one on eBay. Or if you really want, contact a local Ibanez dealer and ask if they can order in a replacement for you.
You could also go to a hardware store and see if they have a short machine screw that fits. Sometimes it doesn't really have to be made for guitar purposes to fit the bill. I once lost a locking screw for my TOM and found a replacement part in a store that sells RC toys.