Tried that, hangs on "loading..." when I enter flight mode from tracking station. (upd: SDL_DYNAMIC_API fixes that but then it turns out that the game won't launch at all because of some weird regression in unity3d https://issuetracker.unity3d.com/issues/linux-crash-in-unityengine-dot-input-dot-getjoysticknames-when-controllers-with-comma-in-name-are-plugged-in ; i guess i'll just stick with mouse until next version of ksp)
Judging by what I see, this problem exists for quite an amount of time and is still not fixed. Joysticks are not recognized, or maybe are recognized but are not configurable... many different cases. Did devs give comments on that? Is that KSP or Unity fault? Do I have to wait for the fix patiently or maybe it's better to throw out my gamepad and use mouse like in the good old times?