You are right. Moscap can not be used at places where the linearity is important. Meaning, if the voltage across it is time varying, then the non linear cap takes non linear current resulting in harmonic voltage generation.
So, wherever the linearity is very important like in high resolution ADCs etc., moscaps cannot be used. If the linearity requirement is not stringent or not at all important like supply decap, moscaps can be used as they give high density. Of course, the value or density depends on the average voltage across it.