You don't become disqualified from the other academies, until you ACCEPT an appointment from one.
But as mentioned, a nomination is only good for the academy that you were nominated for.
Most senators and representatives ask you to list/rank the service academies that you are applying to, and the order of preference. Believe it not, not everyone applies to all of them. I know quite a few people who only applied to one.
Your biggest question should be: If you receive an early LOA, say from army, and you really want air force, even if you received a nomination to air and army both, there is no guarantees that you'll receive an appointment to air force. However; an loa most times is a pretty automatic thing once you receive the nomination. Assuming you accept it. So, do you sit on the LOA until after nominations are handed out and stall on accepting the appointment with the LOA;.... or do take your chances and hope that you receive an appointment from the air force academy.
Some applicants, my son included, made the choice very easy. He applied only to the one academy he truly wanted. Now; if his priority had been simply to SERVE, and it didn't matter HOW, then he would have applied to the others. But he specifically didn't want this choice of having 2nd best. He planned it all out.
1. Apply to the air force academy.
2. Follow their recommendation to try and complete the ENTIRE application in 45 days. (He did it in 34 days).
3. Apply simultaneously for his presidential nomination, as well as the senators and representative.
4. If he doesn't receive an LOA or appointment by November, apply for an ROTC slot.
5. Get interviewed by senators and representatives in Nov/Dec.
6. If no on the appointment, hope for the ROTC
7. If no on the ROTC, accept one of the other universities that he applied to.
8. Join ROTC in college; even without the scholarship and seek a commission to the air force that way.
9. If ROTC turns him down, finish degree and apply to the air force via OTS.
That was his method. He didn't want to compromise; he wasn't doing it just for the free education; and it was going to be air force or nothing. Fortunately for him, he only had to go to #3 above. He received his appointment at the end of Oct and had the BFE the first week of November. But that was the checklist on his wall in his bedroom.
It ok to have preferences and rather have air force over one of the others. But if you receive an LOA to one of the others that you applied to, you need to be prepared to deal with that decision. Or risk the chance of losing out. You won't be disqualified from the other academies if you have an LOA, but you are correct that your MOC might not nominate you to ANYTHING ELSE. You also have to realize that if you do get the nomination for the LOA, and they offer you the appointment, you might not get to sit on it forever waiting for the other academy to possibly offer you one. Especially next year with so many cutbacks in slots. The academies are going to want to know as soon as possible, so they can decide whether to send MORE appointments out to the alternates. Best of luck to you. Mike....