I think the GreyJoys will only be a big enough factor to come invade the reach and stir up the reach.
Its pretty clear Dany is never sailing across the narrow sea. We are basically killing time for Drogon to grow as large as Balerion, and she is going to ride in there scorched earth. Never knew why I felt it would end any other way.
You may be correct, but it seems there is still the Greyjoy fleet if there's any of the unsullied left to ferry across. She will definitely need loyal protectors as the dragon while very powerful, won't keep her from all harm. Those could easily come from allies made once she returns as well tho.