hmm, i can't imagine them fighting for 150 years, or the imperials not stepping in and stopping it.
There was some daedric princes in skyrim though? so why not? but i doubt hircine would start the hunt again only 200 years later.
No, I'm saying that we KNOW they got along well enough for the first 40 years (from the eruption of Mt. Vvardenfell and the whole incident in Vivec through the novels) and I'm sure the peace was kept through the next 150 years, but with Windhelm's relatively close proximity to Solstheim, their influence could very likely be felt there. Perhaps as a backup base or something?
Also, there's no way the Empire would even be able to step in with all of their problems with the Aldmeri Dominion and their utterly weakened state since The Great War. UNLESS, of course, the Empire took the island back in some desperate land-grab since the Aldmeri Dominion took so much of Southern Tamriel, including parts of Cyrodiil, as well as parts of Hammerfell.
Also, they Daedric shrines are in Skyrim, yes, but Daedra can't physically enter Mundus without help, i.e. being summoned.