Even if it's not a windows thing, I can vouch that it is not easy to overcome. Input handling gets hairy really fast, especially in something that handles as many input devices as it seems Elite does (I know because I recently wrote an input system myself). The real problems come not from just bumping up the limit (eg, from 32 to 64 or 128), the problems come from there being a limit at all, and switching to having no limit* is most definitely not a trivial task.
* no [practical] limit in the game, that is. The OS itself might well impose a limit, or the hardware protocol (USB HID). I say "practical" because you still get limits impose by word sizes (eg, 2147483648 for signed 32-bit numbers, but I don't think many people have devices with that many buttons).