Current policy for all the Armed Forces is applicants who have self-harmed being 3 years clear of further instances, but after that it's on a case-by-case basis; the doctors will decide by looking at the reasons behind it.
It doesn't matter that it was superficial, it's the fact that your son used self-harm during a stressful situation, of which he'll be facing more in the RAF and not necessarily combat situations. It was during his exams and, whilst he has got through some hurdles since, even training could be hard for him; being tired, under pressure to complete tasks.... Extend that to work and potentially coming to the end of a 3rd consecutive 12-hour night shift, and you've got the same conditions.
So, there's nothing to stop your son applying again after the 3 years clear and he can use the time until then to work on his fitness, and be involved with activities that show responsibility and leadership potential. However, there are no guarantees that another application to the RAF will be successful, or that he could get into the Army or Navy either, and that's you come in! Your son needs to understand why his self-harm may stop him joining and not make the RAF his sole focus. He should have other career options and, if he does apply, he'll need support if he's unsuccessful again. Wishing you both all the best!