I might pick up some shimano hubs that have oil ports, but one is missing the cap. Is this a problem? I imagine finding a new cap would be a bit difficult.

The only problem that I can see is that it will allow some fine dirt and moisture to contaminate the bearing grease. You may find yourself cleaning and repacking the bearings more often. The rear hub gets dirtier than the front, so if it's missing on the rear, I'd transfer the cap from the front hub. If these hubs are not new, I'd overhaul them in any event. The oiling holes really are not needed, and hubs should be overhauled periodically using grease as a lubricant. If you don't care about cosmetics, you can simply plug the hole.