I always left game discs in the system (and by that, I mean I did this for every game system I've ever owned). Doubt it caused any damage to the thing.

well i left the disc in the wiiu but i might start retaking them out again if im not going to be playing it lol because the extra light gets to me sometimes

however i usually leave the discs in my 360 non slim model and ps3 but now that i think about it upon turning it on it has to do more work to function in a minute plus FIRING MAH LAZER BAHHHHHHHHHHHHHHHHH ahem to read the disc and every other readable thing at the same time producing wear and tear faster might be the reason they say its not a good idea to leave em in case it has a problem of its own and youll have to send it to them with the disc still inside?

anyways then again if thats entirely true then why have the disc in the sytem light in the first place right?

hope that helps because i never given this much thought my self and ive always done this out of habit and had no problems since i take care of them well