I carry a small jar of Vicks with me in my one quart baggie in my purse. I have done so for years with no problem. So there is no difficulty getting this through security in a carry-on.
It is, of course, not possible for the captain to adjust the cabin pressure when landing the plane. I also believe this is a problem that an ENT doctor should address with your wife.
I assume she has tried the typical remedies such as chewing gum, sucking on a mint or hard piece of candy, and swallowing with her mouth open? I do not use Vicks for this purpose and have never heard of using it like this, but I suppose it would not hurt to try this either.
It sounds as if she has some type of blockage in her sinus passage. Hopefully your doctor will be able to diagnose the problem.