Anybody know for certain if this game does or does not support DirectInput?
It doesn't support DirectInput. Mark of the Ninja was developed for the Xbox360 and then ported to Windows. That's why it uses the Xbox specific controller library Xinput. As Windows supports this library since XP as well there was no need to write new code for DirectInput (other than natively supporting other gamepads). Klei was confident enough with other gamepads running through Xinput, even though they will be recognized as Xbox controllers and the initial layout might be awkward. Here's Klei's official statement on this:
Does your game support my gamepad / controller?
Mark of the Ninja officially supports keyboard and mouse and Xbox 360 gamepads.
Other gamepads / controllers will usually work, but they will assume the layout of the Xbox 360 controller. If the layout is wacky for your controller (buttons in the wrong spots), most modern gamepads support custom button layouts with their included software. Check your manufacturer's website for more details.
If you're using a controller that requires special home-brew drivers, mods or adapters to work (PlayStation Dual Shock Controllers, Snes controllers, Original Xbox Controllers etc...) we can't guarantee support. We simply don’t have the hardware to test all of these issues. You're always welcome to post your issue since we might have a solution, or someone from our community might chime in.
If your controller isn't detected you can use the X360Ce tool to force the game to detect your gamepad as an Xbox controller. See here: http://pcgamingwiki.com/wiki/Controller#X360Ce