As of todays date Oct 30 2012, I can confirm same observation.
Tested one of these consoles with several different types of mines.
Damage specific projectile damage consoles work on mines and torps, but these do not work at all.
It's not just the variable geometry detonators it is all ship consoles and I have contacted Q&A multiple times about it and got no response whatsoever. Energy weapon ones work sometimes but then they stop working but all other consoles I have tried do not add the buff they are supposed to.
I also have a warhead yeild chamber and a console that improves turn rate RCS something or other and neither of those are working either. I have no idea if this is just a display issue or if the buffs are not being applied.
The only console that I use that works without fail all the time is ablative armour