It varies. Stardock certified mods should always be safe to use. Uncertified mods are much more fluid, and some are gamebusters on the metaverse. There may even be certain combinations of Stardock certified mods that, together, may cause flags to be raised.
However, simply poessessing an uncertified mod is unlikely to be an automatic kickout. It's how you use it that determines if the game is valid or not.
All Stardock certified mods should be fine. I found only one exception. When you use more than one mod and your planet quality ability gets above 40% (i.e. your society ability, not the local planet PQ boosters, you can check that in the "Domestic policy -> Stats" screen. There are parties, improvements and technologies which improve PQ.) you get a abnormal flag, i.e. zero points in Metaverse.
Not certified mods are usually fine as well. I did not have problems yet. Does anyone have a example wher you get problems?