All class abilities and ultimates are considered spells in the game.
If you're having issues with negate or other silence effects try CC breaking or using the active Heavy Armour skill to make yourself immune.
The abilities use spell damage (maybe weapon damage now as well? was that a change?) and spell crit however.
I would be fine for ZOS to make more changes for ultimates however, I really dislike that the mages guild one can be reflected by a DK.
The whole point of Negate is to remove these kinds of effects.
It would be absurd if Bat Swarm couldn't be silenced.
You just don't want people to be able to use counter-play against you.
In other words, L2P.