It entirely depends on the individual. There is a wide range of intersex conditions as well as a wide range of non-binary genders. There are some intersex people who are very similar to one of the binary sexes, with just a small physical change, while there are other intersex people who are more in the middle. There are certainly some situation where a non-binary intersex person wouldn't be cis. For example, an intersex person who looks mostly male (to the point that most people would read them as male), but this person identifies as a feminine aligned non-binary person. I doubt that this person would consider themself cis, even though they are intersex and non-binary.
I also know there are some intersex people who identify cis. For example, there are some intersex people who identify as binary men or women and consider themselves cis, because they were raised as men/women and didn't find out they were intersex until later in life. And there are also instances of intersex people who identify as non-binary and consider themselves cis. (I feel this would be more common for people who are more of an "in between" intersex, but I don't know for sure.)
There are also some intersex people who feel as though neither "cis" or "trans" apply to them. So while there are some non-binary intersex people who consider themselves cis, there are also some who don't. It depends on each person's unique situation.