I have noticed that since the last patch whenever I get my weapons knocked out by Subsystem targeting I cannot fire my AUX Cannons, this should not happen as they take power from AUX instead of Weapons

So now my Cannons are able to be disabled when either my Weapons or Aux power is knocked offline, please can you change it back so that AUX cannons and associated Boff powers are available if you lose weapon power as they should not be affected

That was on purpose.

If I remember right, it had something to do with weapon system and not weapon power.
In your case, weapons are offline, including those powered by auxilliary. The benefit being if your weapon power is just drained, your aux cannons are not.

The primary reason the Aux Cannon was "patched" was because people were using the invulnerable quantum bubble followed by EPTW to allow them to start shooting again while completely immune to all incoming damage. Talk about mad 'SPOILTS!

imo the real exploit with the aux cannons is simply not using them. I strongly believe that the aux cannons are added to the vesta pack as a balance move, so people would actually think they are useful (though they are useful in pvp, but for general purposes, which most people do, the aux cannons are not the best, understand this pls )