I agree, strategic bombing has proved ineffective generally, but when you add WMD into the mix, things might change. Not saying they WOULD, but if fortifications are as tough as Chris has suggested, then planets will be virtually unassailable, and the Vaylen would eventually need to move onto depopulating a large enough area to begin staging their Hoth style assault.
Also, If I’m a Forged Lord, you KNOW I’m going to put my anti-invasion Q-beams in the middle of cities.
As for the engineering difficulties of submerged fortresses, how about truely massive submarines? They can manouver, fire into space easily, and have hundreds of meters of water between them and the surface.