I've done it and it doesn't change a thing aside from the obvious functionality-wise, which is to enable the pistol to fire without the magazine in place.
A magazine safety has no business on a pistol you may need to rely on in a crisis situation and I avoid them if possible or remove.
In fact after carrying my LC9 in an DeSantis IWB last summer and prior to removing it, enough crud, lint and perspiration had apparently worked itself into the channel the mag safety resides in that it became frozen in the forward, or deactivated position.
I had to use little CLP in the area and work it back and forth to loosen it. That's when I decided it didn't need to be there anyway.