As a player who likes to use both, I have recently been evaluating my strategy and it seems to me that Ballistic missiles are superior in almost every way. They:
- Can only be intercepted by TDS. Sure SAMs and AA guns can do a little damage, but not enough to shoot it down. Bombers are vulnerable to all of these as well as fighters
- Cost no man power, thus if one is shot down, you sustain no casualties
- If I'm not mistaken, Bombers are best for taking out infrastructure. Ballistic missiles do this as well without putting manpower at risk.