There is a downside to survival bonuses. Often times the side with the upper hand pushes the fight so far as to follow a fleeing enemy for sectors simply to deprive them of bonus points on landing. It can (in some situations) simply reward the side with better planes, better numbers, or whatever, because they simply will be the last ones standing to land and get the bonus.
Overall I'm for them, but I think both sides of the coin must be considered in any setup, rather than say "always use 'em."