Is there any way to have the nintendo joy-cons compatible with the controls?

While I haven't test it myself, I'm sure JoyToKey would work with the joy-cons. The game's controller detection is kind of bad.

It does seem to work, however i am unable to use both joycons, is this a bug or am a literary unable to do anything about it?

I believe JoyToKey has support for multiple controllers, which I'm guessing is what the Joycons work as. I'll verify it when I get the time (and remember).

Edit: Yeah there's a "Joystick 2" tab. Maybe it works in there.