Some questions are asked over and over. Which is why we can tell that you didn't do a search or take ten minutes to read a few threads - you couldn't have avoided finding the answers if you had. You'd also have gotten a quicker answer if you had tried searching.
Super SU won't increment Knox by itself. The flash counter per se can be reset. It's a widely respected and robust app and you didn't give any specific reason why you wouldn't want to use it. If you remove Super SU without manually adding more cumbersome alternatives, you won't be rooted anymore. If it is your intention to remove root, then go ahead. If you want to remain rooted, then you should do some reading as it would seem that you don't understand what Super SU does.