A deadline is a deadline. The process of applying to any SA is intentionally a very long, complex and frustrating process. It separates the competitive from the non-competitive records. There are other prospective candidates who are also in your friend's position (missing a deadline) and many who began the application process as early as January of their Junior year in high school (depending upon your state of residency) who have yet to receive a nom.
There will be many who have submitted their applications early, done quite well on the CFA, had glowing recommendations and received multiple noms who will not be offered an appointment.
One option open if their parent is active duty or reservist who meets the criteria is a Presidential nom. Other than that, this being one of the most competitive years, failing to meet a deadline will not bode well for those desiring an offer of an appointment.
Though they could complete the application process and hope for an offer of NAPS or Foundation, I doubt an offer would be made since the question of "Why didn't they receive a nom" may be asked. My advice to your friend, if they are really determined to attend a SA and are applying for the right reasons, would be to apply for next year's class.