Here in the state of Indiana we even have examples of this, there are many towns, physica features, etc. with indian and french names, but those people of been gone for 200 years. We keep the names though, because that's the only thing we have ever known to call those places. (And don't give the THIS IS NOT EARTH!! AHH! I WILL DESTROY YOU FOR COMPARING THIS TO EARTH! I HATE YOU! YOU ARE MY ETERNAL ENEMY! response, because this is something that would have no reason to be different in Tamriel.) Also it should be mentioned to lengthen the comparison that many of the people in this area are of German decent, and really dislike the French and anything to due with them, yet they freely live in towns with French names!
Also, I do not believe that Vvardenfell would be a name the Imperials applied to the Island, as it is not in keeping with the spirit of Imperial names. If the imperials named the island something other than what the dunmer had previousely called it, than I believe it would have a more imperial sounding name. Also, I strongly doubt that they would have used the dwemeri name either.