In my graphics options it says mouse is enabled (but text field is not selectable and is red. I have disabled Mouselook, and still no mouse. I can tell its "working", because when I move my mouse it highlights menu's etc. I just can't see it.
It's intentional. If it's just dot over destination... wait for docking and exploring there's not much too it. The lack of vector and even target arrows for off screen targets is all pretty deliberate to give your brain a bit more to do between A and B.
Same issue here. When I play in 3D SBS the mouse cursor option in GRAPHICS is greyed out... I can mouse look but I can't deactive it by pressing mouse button 3 and use my mouse to steer the ship... prior to the last update everything was fine in 3D SBS...