So this is interesting.. I have both. The SNES Classic I have is fine to use (I also recommend using the CRT filter, otherwise the graphics are too pixelated), I haven't checked the kernel version it has.
The v2 of the NES Classic is not, I can see a difference on the monitor backlight.
V2 uses the SNES logic board now (v1 was a marginally different board) so the difference must be either kernel versions which I haven't yet experimented with switching around (you can) or a marginal hdmi output or an interaction with whatever software they're using on this revision with the snes logic board.