I can't answer for your 6946, but there are several semis out there that have the mag disconnect. My Browning High Power used to have it - I took it out for 2 reasons, (1) due to the placement, the trigger release rubbed on the mag itself so the trigger was harder and grittier than it needed to be, and (2) I didn't see it as a safety feature.
With the mag disconnect in, you can't do an effective tactical reload (leave the last round in the chamber when you change mags - eliminates the need to release the slide since it's already in battery when you swap mags. If you have 10+1, and the +1 is in the pipe, then fire 10. #11 is in the pipe and the gun is ready to receive a full 10-round mag.). The benefit of the tactical reload is that even if there is a hiccup in the reload process, you still have one round to fire if you need to.
If I had to guess, the disconnect shouldn't affect anything else as it is likely something that's commonly removed. Just know removing it will likely void whatever warranty you have in the gun.