For the temperature it really depends how long the system is on, in standby though I'm not sure but there was a case of someones wii overheating and breaking from standby.
Yes the slotload LED's are SMD.
I imagine it would cause some trouble, i don't think Nintendo would put it there for no reason, but cutting into the shielding won't cause problems.
Just so you know no talking about chips here we want to keep everything legal.