Ok, so nobody bothered to answer my question about C64 joysticks, but I thought I'd post the idea anyway. Actually, I realised after my post that Pertinax had found the same solution earlier, to use the Shredz64 control adapter.
This is the main summary of the Shredz64 project from its homepage:
"The Shredz64 project is an attempt to build an interface to connect the Playstation Guitar Hero controller (and any other PS controller) to the Commodore 64 computer, then create a Guitar Hero like game on the C64 utilizing the guitar controller."
So if we use the PSX control converter for X-Arcade, and plug it in to the Shredz64 PSX to C64 joystick converter (known as the PSX64) we'll have a way of using an X-Arcade stick on an Amiga. This way all games will work without modification (WHDLoad, etc...).
I've just e-mailed Toni Westbrook (creator of the Shredz64 project), let's see if we can get this solution off the ground.