can I connect a joy con to my pc to play hacks on snes9x?
You'll need to get the joycon connected to windows first, so that your PC recognizes that you have a controller device connected. Then, you should be able to configure the input in snes9x, and hopefully the joycon will be connected. I have not tested this personally though.
This tutorial shows you how to connect a joycon to your pc.
This tutorial shows you how to configure snes9x inputs.