Simulator control surface project- advice needed (lots of digital inputs)

Have you considered using either the arduino pro micro with a diode matrix instead or the Leobodnar boards?

Using the pro micro and the mmjoy software (http://simhq.com/forum/ubbthreads.php/topics/3899105/mmjoy-mmjoy2-build-your-own-usb-controller) you can have more than enough inputs for your project. I myself am considering to make an F5E control box for the main functions and I am planning to use this method.

Leobodnar boards (www.leobodnar.com) come in various sizes and characteristics (to build a joystick, button boards of 32 and 64 buttons, etc) and use another type of SW where there is no programming needed.

You can look for both solutions on youtube and you will see there are no issues with the bouncing.

Hope it helped!