Adding support for additional mouse buttons won't break the pilot code (number of controls do, and that's a different thing), but it wouldn't work very well with the current code. Mouse and joystick button bindings are combined, so mouse button presses actually trigger joystick button actions. That means that the maximum number of possible mouse buttons is fixed with the number of joystick buttons, which is currently 32. But because the controls are shared you end up with weird bugs where pressing a mouse button may very well additionally perform a completely different action which is bound to a joystick button with the same id. Fixing that properly, which involves adding an additional id just for mouse buttons, does require new pilot code though.
For more mouse button support now we just need the input and event code upgraded to handle it. So it is possible to do, I just don't think anybody really wants to jump in and do it that badly considering the control binding bug.