An LOA can be given at any time, for any reason, with or without conditions - but it’s not something to look for. Most cadets and midshipmen never received them.
Yes, you wait. USNA has a cap on numbers of color blind waivers it will grant each year (a handful, usually in the teens), and they probably wait for all applications to come in, then assess the color blind DQ group as a parallel competitive group to whatever competition they are facing in their nom group.
If your son does not already know this, those who go into USNA with a color blindness waiver will be informed that certain communities in the Unrestricted Line family of offficer warfare specialties will be permanently closed to them, such as aviation, submarines, surface warfare. That group is provided opportunities in Restricted Line (intel, cyber, oceanography, etc.) or Staff Corps (Civil Engineering, Supply, etc.). They can also go Marine ground (not aviation). The needs of the Navy will dictate what is available. If he wants a full clarification on this, he should call USNA Admissions and have a candid discussion. These appointees go into USNA knowing their options are limited, but go they do.
He should also have additional alternate plans. NROTC uses the same DoD military medical accession standard, and color blindness would also be a DQ. It is my impression NROTC gives few to no color blindness waivers; career opportunities would be similarly limited. Marine option, ground, would not be a problem.
it is my impression USNA, USCGA, USMMA are the most stringent on color blindness and no or few waivers. USMA and USAFA seem to be more flexible. It’s not a frivolous difference. Waiver policies differ because operating environments, missions, gear and equipment differ across the Services.