Sam, he wasn’t referring to the Sefer of the Ramak, was he? I don’t know what he saw, but he definitely wasn’t complaining about a Zohar Hakadosh.
But again, where do you find that he had a problem with Nissim? He held Malachim are not related to the physical and therefore cannot be seen. This is why he explains all such visions to be dream state. But, where do you find that he had a problem with Hashem performing Nissim for His close ones, as in fruits growing out of a tree, raining on particular spots that were pointed out by a person, being saved from falling off a high roof, or knowing a strangers name?
The Rambam did not believe in Kishuf or Sheidim perhaps, and calls such references Daas Yachid, but someone who can’t comprehend a Ness is not based on the Rambam.