If yes, I think I will have to interrupt ground trace of the mini-joy button and wire it directly into the matrix. Is this correct? Or is there any way how to use preassembled connector with MMJoy?
Well, I will not try "reinvent the wheel" to made MMjoy2 compatible with this PCB. As you suggest just cut the PCB trails that go for button pins an wire two pins in MMjoy Matrix or Shift Register, as MMjoy2 expect.
In this micro switches 2 pins in one side are interconnected internally - probable for redundance - select one fin from each side.
