I am still waiting on my card arriving but I have just received the following information from Dirk Jagdmann the author of the linux joystick and keyboard drivers
"I updated my MK3 drivers to MK4. However they currently don't support any of the new features the MK4 has. The plan was to merge my joystick,keyboard code with the SID code that simon white wrote, but as there are currently still some issues we have not released anything yet."
So I guess I we will shortly have Linux support for the joystick port even if we have to wait a while for windows drivers.
So I guess its time to give e-uae a try.