So I was exploring Fort Snowhawk with my conjurer earlier and in the final room which looked like a sumoning/ritual room for the necromancers that were holed up there I ran into a Acendant Necromancer. He was very powerful and difficult to deal with even at level 17. It took me at least 5 reloads to get the best of him, even then it was not easy.

Does anyone know what the deal is with them, was he just a much higher level than my character or do they have some high resistances to magic?

Maybe you need higher magic resistant.

I met one at the Shadow Stone and my Two Hander took him out easily.

Skyrim isn't really safe until level 40-50, it all really depends on your skill use. I strongly recommend the Lord Stone.

Dual Wielding Bound Swords, Summoning Dual Dremora Lords, Storm and Frost Atronachs, Spamming Flaming Familiars. A Flaming Familiar explodes as it is replaced by another, it can be an expensive method of dealing with Summon thieves like an Ascendant Necromancer, but Sheogorath does get teary eyed when it is happening.