Okay, so it's been a long time since I played AHQ and my memory is terrible, but I'll give it a try
The surprise roll mechanic is related to who gets to act first in combat, monsters or heroes.
IIRC it also affects monster placement.
During the exploration phase the heroes may open a door to a room, if this room contains monsters then the combat phase begins, starting with the surprise roll. There are various modifiers to the roll, including the bonus that the skaven assassin has.
One the advantages of the assassin's placement rule is that he can attack the heroes from the corridor, meaning that it can avoid the potential bottleneck of the doorway where all of the other Skaven will be attempting to get to the heroes.