Blind spots will abound regardless… planets are huge, and you can’t build a fortress that points in every direction (at least not an affordable one). The strategic function of fortress worlds is to make “safe harbors” from which human hammer assets can strike and harass Vaylen penetrations. One of the odd facts about Iron Empires naval operations is that you can’t make your opponant fight if he has fuel to operate at HEx. If you close on an unwilling foe, zip, off he goes. So Fortresses aren’t designed to be a “wall”, stopping enemy Hammer forces cold, but strong points beyond which it becomes dangerous for the enemy to penetrate. Doing so exposes the long trains of logistical transports following the spearhead to harassing attacks.
As for nuking fortress worlds into glass, it’s expected that a desperate enemy will go full out against a fortress world when it comes to a siege, throwing everything possible at it. The populations will have some sort of underground shelters (if their lords are humane), or flee in civil spacecraft, or die horribly, which is still preferable to being hulled. As Faith says, “It’s a fortress world, it’s supposed to be ruined.”
As for the Q-beam, it is similar to traveller’s Meson Gun, in that it creates a “tear” in the positive universe at a distant point, without regard to intervening matter. The trick is that the point at which the tear opens has to be a virtual vacuum. The tear won’t occur if there’s too much positive matter in the vicinity. The same technology (on a much smaller, more controlled level), is used for distortion drives. So distortion drives can’t operate inside dense particle fields either… near planets, in gas clouds, nebulae, etc… Furthermore, HEx, which is more sensitive than subluminal expansions, generally requires that you get outside of the star-system’s particle disc in order to fire up the drive (trivia: the quickest way out of a system’s particle disk is “up or down”… so that’s where system defense forces station the bulk of their assets: the North and South Watches).
I could obviously go on at greater length, but I have to paint today 
Chris