Managing applications through Configuration Manager in Intune
Anytime you perform any operations on a system that is a performance impact. Whether or not that creates an "issue" depends on your definition of "issue" and what exactly that operation does as well as what else is also impacting performance in the environment and the systems where the operation is running. Thus, there is no definitive answer here for any given organization. You will have to test and see.
I suggest starting with a smaller subset of systems and a much tamer interval and then increase both as you are comfortable that there are indeed no impacts keeping mind that there are other environmental factors that could impact perf at various times.
Without knowing the details here though, it sounds like you may be addressing a symptom and not a cause here so you may just be chasing your tail or compounding some other issue.