It's the same way in any gametype. For instance, in U4E-Fortress, the late comer might face a high level Mage, and even in normal UT games, the late comer won't have all of the weapons and armor that somebody else would have that's been there since the start.
It hardly matters anyways, because no many people are going to play on servers that keep a game running forever.
And even more importantly, well the new comer will only have a few Bucks to lose if they get killed, the Fat Cats will have TONS of money to drop! Just think about that for a second. Just getting one frag on somebody with a ton of dough will make you set for the rest of the match.
Also, you don't get to keep the weapons after you die, you only get to keep half of the money you earned. So really, this game does tend to favor the late comer to some exstent.