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When I first started the game my SN30 gamepad was not recognized, but my X-Box 360 controller worked fine. Turns out, I just needed to add an entry to the .local/share/SteamWorld Dig 2/gamepads.cfg file:

03000000c82d00001290000011010000,8Bitdo SN30 GamePad,platform:Linux,a:b0,b:b1,x:b3,y:b4,back:b10,start:b11,leftshoulder:b6,rightshoulder:b7,leftx:a0,lefty: a1,

Hope this helps someone.