Supersonic speeds would certainly be used for beyond visual range (BVR) engagements. Higher speeds mean you and your missiles have more energy and maneuverability. Since the F-35 needs to use it's afterburners to reach supersonic speeds, it likely wouldn't use the extra fuel just for transport.
In my (limited) experience, the inaccuracies are just due to amateur pilots/ATC not getting phraseology spot on and being more forgiving than the real world. Obviously, VATSIM doesn't have the users to populate the server with true to life Traffic and ATC at all locations. This lets you make your callouts slower than what you would see in real life.