The majority of leagues that have commissioner veto have it to prevent the league from vetoing every deal. I know I have it in my leagues because I don't want every trade that might help a team gunning for the championship shot down by the other teams trying for it.
However I wouldn't join any money league that for anything over 50 dollars without having some knowledge of who was in charge, without there being a independent party involved. Yes I do run a money league, but the fee is only ten bucks.
There are some ways to tell if a league is on the up and up though.
If its a keeper league, check its history after joining, if each year the league has to replace over half its teams something is likely up.
Talk to as many owners in the league as you can, if you find out a high majority of them are related its also probably trouble. Even if its completely legit I'd still probably avoid a league like that since family would likely be far closer then some stranger they just met.
If its a money league check the past years and see if anyone made a post about receiving their winnings. I make it a point to have the winner post this so the rest of the league knows I'm not pocketing the money, though I did win three of the first four seasons that the league was a money league.
If you have a bad expirence don't assume every commissioner is out to rob you blind because of it. Before you agree to join a league see if you can talk to the commissioner for a half hour or so on IM just to get a feel for them and their league. For every commish like this guy there are a 1000 that want to have a great league.