Quote - It didn't ask me if I wanted smart props. Perhaps because I was saving multiple props?

Yes, that's the reason. Poser does not give you the smart prop option when you use "Select Subset".

Quote - However, the eyes are not parented to the head as they were before I saved them.

Is there a hack I can do to the prop file that will make them automatically parent to the head like a smart prop?

Yes. Open the pp2 in a text editor. The parts that parent to something external to the pp2 (eyes and point target) will say "parent UNIVERSE", change that to "smartparent NameOfExternalParent", eg "smartparent rEye". The parts that are parented to items in the pp2 will be assigned to the correct parent, but with a normal "parent" statement. You need to change every instance of "parent" to "smartparent".