One way of interpreting Fortification is to say that it only affects crits and sneak attacks, so that's it. Nothing else is mentioned, so stunning attacks still work.
Another way of interpreting it is to say that it gives you an X% chance of being immune to crits (per hit). Since stunning attacks don't work if you're immune, it indirectly protects against these attacks as well.
Use the one that seems most intuitive to you. Personally, I lean towards the latter.