if it was that simple, the Dominion could have easily destroyed the Empire in the initial attacks on Cyrodiil. Magic is powerful, but training people to get that good with it requires very long periods of time and there is going to be limits to their number. Making an entire ship invisible would be very difficult and take a lot of resources, all of which would be potentially lost because of the difficulties of just getting there.
Magic isn't an "I win" button the way you present it. If it was, the Thalmor would be in charge of Cyrodiil.
This summarizes my thoughts rather well.