That’s a cool idea. There are nasty engineering problems building underwater, so I’m not sure “most” fortresses would be submerged, but I’d think a lot of Forged Lords would consider the tradeoff (more construction cost for better defense) to be worth it.
And even with hardened-and-shielded fortresses, you’d want to conceal or at least obfuscate your exact location, because you don’t want to make it easier for the enemy to drop that asteroid or H-bomb on you – and they’re certainly going to try to.
As an invasion force commander, especially a Vaylen one, I’m going to do everything I can to smash the fortress itself before resorting to exterminating the populace and hoping the defenders relent. Besides the waste of valuable slave labor/hullable humans, the problem with such terror tactics is that they rarely work: The population tends to rally, not collapse (consider the Blitz in London), and even if they don’t, the defending military secure in their bunkers doesn’t really have to listen to them.