Good point, I forgot about that. Though what I had in mind was more of a suicide attack scenario. If acid tubes are rapidly draining your health, all you may have time for is to toss a nade and get out, so putting a few rounds in the OM on your way out/before you melt might be useful.
But yeah, if the base is improperly defended and you can stand in it comfortably, it looks like you should take down the eggs.
Although, if you take down some eggs, critters can always come out of other eggs. Aliens generally have more eggs than they tend to really require, for survival purposes. Humans tend to have just enough so as not to cause a backup in the spawn queue. So killing a few eggs might be an inconvenience at best (if it's not SD).
Killing the OM, however, makes everyone coming out of the aformentioned eggs unable to evolve, so you won't get flash mobs of dragoons coming at you again and again in your assault because they evolve as fast as they can right out of the spawn.