If you have an LOA and a Pres nom, that's all you need (from a nom standpoint, that is). I understand why USNA might want you to apply for other noms, as it gives them more flexibility. However, at some level, I can see why the MOCs (well, the nom committees) might feel the way they expressed themselves to your son. From their POV, your DS didn't need their nom because he already had one and only needed one (with an LOA). Thus, they might feel he would be taking one from someone else.
The above said, IMHO there were far better ways to handle the situation on their part than what you described. They should have started by congratulating your DS and then explained that, because he had an LOA and nom, he didn't need an MOC nom and they wanted to use their MOC noms for candidates who needed them, including LOA candidates w/o Pres noms.
Some MOCs may have so few qualified candidates that they want to give folks like your DS a nom just to fill their slate. But if they aren't in that situation, it is better for the overall "process" for 10 other candidates to receive that nom.