Ok, so after some testings I came to the following conclusions:
smogas is partly correct. The abilitys are actually added to the unit, but in no way accessable, neither via UI nor through triggers. In uprooted state that is.
This only applies to Active Skills though, Passive Skills are shown and work.
Also you cannot use the "Ability being cast" event. Actually you can't use any ability detect events, instead you have to use Order events.
I've attached my testing map. It also includes a simple way to remove/add abilities when root-/uprooting. It may be in JASS, but that's only because i'm lazy and it's easier/faster to write. The same thing in GUI is pretty easy =P