Balancing D-weapons is a really, really simple thing to do from a rules perspective, and was talked about during the playtesting of the initial apocalypse release.
1) D-weapons auto-wound and auto-penetrate.
2) They auto-explode.
3) They count as St 12 for the purposes of instant death.
4) They dont:
-Ignore cover. Though this rule could be combined on certain weapons.
-Ignore invulnerable saves. Though this rule could be combined on certain weapons *mostly vortex*
-Cause instant death, though this wouldnt be an uncommon addition.
-Do multiple wounds. Though this could, and likely should, be combined on certain weapons as an alternative to ID.
-Cause multiple hull points of damage normally, though this could be combined on certain weapons.
GWs response:
No, we want them to kill harder and make the game go faster.
Playtesters:
Are you sure?
GW:
Shut up, the books coming out now.
Years of feedback showed the playtesters to be correct. GWs response? Make them ignore invulnerable saves, but give a 1-in-6 chance of not killing infantry, thatll keep people from using them on infantry.
Players: Haha, yeah right.
As for superheavies: Bring back immunity to non-strength-to-damage psychic powers and special abilities unless they specifically state otherwise would be a good start.
As would bringing back poisoning only on a 6+ for GCs and haywire glancing on a 5/pen on a 6 for SHVs.
Otherwise SHVs arent bad for their price, nor are they excessively good- if people complain about them, it tends to be the D-weapons, as noted above.
As for fortifications... no explodes result would be the simplest solution to everyones problem, as then they wouldnt care about D-weapons and would slowly degrade over time, as the now-dead gods intended.