I've had all my joysticks mounted via wood screws for a few years now, and never had a problem.
A few things I would point out though are:
1) I used 1x poplar (3/4" actual thickness) for all my modules.
I think the results with MDF would be less durable than solid wood.
2) I used 1" #10 screws with the tips cut off of them with a dremel tool.
That lets the full length of the screw be near maximum diameter, rather than relying on the pointy part of an unmodified screw to hold them in.
3) Durability will be more influenced by who plays your machine, and how they play, than anything.
If you have a bunch of people that are respectful of the controls, they will hold up better than if you have a bunch of people just beating on them in frustration.