I'm a bit confused by this post, since some of it reads as if it's about you ("my future trip") and some as if it's about your son ("unable to add the flight to my son's account"). I assume you know that you are not supposed to earn miles for your son's flights and vice versa, though some sr./jr. pairs have reportedly gotten away with pooling their miles in this way (as long as they're not both in the air at the same time on the same airline). Perhaps you could clarify who's who and who's doing what here?

If this is about your son, then based on a lot of personal experience with a badly screwed up name:

1. It may affect the check-in agent's ability to find his reservation by name, and hence to issue a boarding pass. Have his reservation code (usually six characters) available as an alternative way to access it.

2. It may affect automatic frequent flyer credit, since he may fail the computer's name-number match. Follow the airline's missing credit process if that happens.

It will not affect his clearing security, in flying once he has been issued a boarding pass, or in any other way.