I've played a lot of 3-player games and no, I don't agree. Here's why:
The Artist is actually a crappy character. He doesn't do anything except defend some of your districts, which he doesn't even do for free. Whenever my playgroup tried using the Artist, nobody would pick him at all.
The Assassin does get a 100% hit rate, but crucially there is no guarantee on who he hits. For example, say the three players are Alice, Bob and Charlie. Alice has the crown counter and picks the Assassin. This means she can guarantee a hit on either Bob or Charlie, but she can't guarantee a hit on Bob or Charlie. Say Bob is currently leading, so Alice wants to hit Bob. But she might end up killing Charlie. Since the Assassin (like the Artist) doesn't add any extra value, this just ends up extending Bob's lead. The Assassin is great in a 1v1 game, but in a 1v1v1 game, you have to stop both opponents from winning, not just one. The upshot actually is that my playgroup considers the Assassin pretty bad, and he's not usually picked first.
The Thief can be played around by using as much gold as you can each turn.
If you remove the Assassin and Thief, the most severe consequence is that ganking gets much weaker. Near the end of the game with one player threatening to win, what the others will generally try is to pick the Assassin & Thief to stop the player from winning, because these are the strongest gankers. If you remove them then the only gankers you have are the Magician (and that doesn't even work unless you have weak cards in hand) and the Warlord (but since the Warlord moves last, the player might have build 8 districts already, and the Warlord cannot gank).
tl; dr: don't remove the Assassin and the Thief, and if your friends want to keep picking the Assassin, let them.