Firstly, that partly depends on what happened to the third robot. Did they not show up for the match, or did they have to press the e-stop? If it's the second case, there's no rule that you can't score on a disabled robot's trailer (as far as I'm aware) so if that's the case the alliance with the busted bot is pretty much screwed. Especially if they never moved in the first place and spend the match right in front of the opposing team's human player.
If it's the first case... that's a tough one. It depends a lot on the robots that are on the field and the strategies they use. I'd say that you're right, it looks like the short-handed alliance has an advantage. Not an incredibly game-breaking one, though.