Seeing a thief doesn't stop him jacking you. If you are planning to fight a thief, at some stage you have to accept that blackjack possibility, and it is a reliable skill. I know a player that plays thieves regularly and particularly likes killing duergar, because they always run straight at him and he jacks them.

The thief can use scrolls to enhance himself and mess up the assassin. If he manages to jack the assassin, that's all that's required. Many thieves take thug up to cheapshot, and a hasted mace wielding thief will kill a slowed assassin very quickly indeed.

Bear in mind that thieves have potions to escape. Assassins don't (or shouldn't, if the thief jacked them). That even allows the thief to make use of any preps the assassin is carrying in his inventory. Ultimately, thieves can fairly easily escape assassins with two teleport potions in their inventory. Assassins cannot escape thieves nearly as easily when both players make good use of their skills.

That's my opinion, but I've seen a lot of thief vs assassin fights and been in more than a few.