Replacement of the MoBo is not necessary. Most of the times there are two possible faults when the joystick malfunctions:
1) The soldering has become bad. This is an easy thing to repair, just heat-up the soldering iron and rework al 9 (or so) soldering joints.
2) One of the CIA chips is broken. These can be replaced. In earlier Amiga's they were socket-mounted and therfor easy to swap. In the 4000 they're soldered (I believe). Still a bit of work but do-able and probably cheaper than a new / refurbished motherboard.
You could also try and find an Amiga-user near you with soldering skills who is willing to help you out at the cost of a crate of beer and material-cost.
