All commissioning programs have their own waiver authority and policies.
USNA approves only a handful of color vision deficient appointees a year. Think teens. And - it is made very clear that unrestricted line warfare communities such as aviation, submarines, surface warfare, and some others, will not be open to them. They will have options for restricted line and staff corps communities. There are threads on this every year. Marine ground - no problem.
NROTC - I do not know.
Your son should be very clear on what Navy or Marine officer communities will be open to him.
I believe USAFA does not have color vision restrictions, but he should research all the SA and ROTC programs at primary sources and by calling a unit of interest or SA Admissions.
Your son should also go to the DoDMERB home page and read through the items in the left-side menu, every page, link and drop-down menu, to understand the process.