Actually you blow up drones, mines and pilots...

In level 3 (or 4) you blow up one fighter only, but you have to destroy all of it's subsystems to kill it. However, when in the hydra, you munch them by the dozen, although you can't squish capitals)

It's true that I think that those ships would make a charming addition to the FS2 ship library... aside from several fighters and drones, I have seen one freighter/cruiser (looking very aten-like) and the squid like leviathans. Perhaps in the future, a modeler might see them as worthy of interest...
The game always was a torture, as the story ends up in a cliff hanger. However, if a MOD was to be born, it could stage the pilot's escape from the aliens (I like to call the the chtons, in referrence to cthulhu), the reunion with earth, and the campaign to destroy them (both in space and water)...
Of course those are only ideas... for now, preserving the ships (as done with space: above and beyond) might be the way to go...
Edit: I never thought the game had that much popularity. Should you be interested to know, it's a descendant of "the hive" game by trimark (it shares gameplay, orchestrate music (I love that) and sound effects).