I'm not arguing that it necessarily happened that way, merely that the arguments stated were very poorly constructed.
As for the former, I might suggest two counter would be along these lines: Humans existed on land, and and less agile underwater then on land. However, if they were to spend a few millenniums fighting a race of intelligent sharks underwater, with very little combat on land, might it not be reasonable to expect our fighting machinery to be developed primarily for fighting underwater?
The second counter would also be along those lines: Human may be more agile on land then underwater, but submarines most definitely are not. Our land based nature doesn't carry over into our designs made for alternative environments. The Lucifer is certainly used by the shivans exclusively for real space combat - they never initiate an attack in subspace, in all of FSdom - so if they were Subspace born, the Lucifer and the ships we see may be their equivalent of submarines.
Given the rather unpleasant side effects of any combat we see take place in subspace, it would certainly make sense for a race from there to not want to fight there, just as people from New York would rather any wars they take part in occur somewhere other then New York. Since the Shivans are also obviously very aggressive, wouldn't it make sense for their ships to be designed for the purpose we see them used for - offensive fighting against real space races in real space?
Now mind you, I'm not sold on the idea of them being from subspace myself, but that's primarily because I don't see all that much evidence that seriously supports it.
Ah right: One other thing, the "American can't even find Osama in a cave" analogy. Technology considerations aside, it's important two remember two fundamental differences between the two situations. 1, Osama, even in an uncomfortable cave, has a few basic neccessities reliably provided. He may not have Coke, but he does have air - something which the ancients couldn't be so assured of. 2, More importantly, Osama still has supply lines. He's not setting up a self sufficient society in that cave, just hiding out and sending people to get supplies when and where he can from the rest of society. Society as a whole still exists, and while he may be exiled, there are still ways of getting food, medicine, weapons, whatever from society as a whole. It isn't neccessairly easy to tell the AQ agent buying food to take back to the cave from the rest of the customers at the local food market. The ancients, by comparison, have no market to sneak into. It's been blown to hell.