Will I be logging on to a ship with no weapons after the patch ?
And what about the ground weapons and our boff's wearing full sets and the visuals, will they lose the stf weapons and thus visuals or will there be no post season 7 visuals on them anyway ?
They probably just won't be available at the vendors anymore, like how previous lockboxes don't drop but still exist. And it's only the "standard" weapons with the [Borg] modifier. The MACO, HG, and Omega Sets will just be part of the Omega Rep system. This "retcon" has nothing to do with those, so don't worry.
Also, AFAIK, the only ones with unique visuals were the Set Weapons, weren't they? Of course, I never got a MK XII [Borg] Mod weapon, do those have their own visuals too?