If you are talking about the button hotkeys then yes they are in the screenset as Brett says. However if you are talking about the system hotkeys, things like arrow keys for axis jog etc then they are stored in the .xml.
If you use a custom screenset, like I do, you still dont need to worry as Mach will not overwrite it and when you open the new version of Mach it will look at your xml and load the screen that you last used.
Hood