I don't know for sure but from what I've heard the reason why the navy doesn't allow LASIK is because they are afraid the flap will pop open under intense pressure. So if the cocpit depressurises or you eject their could potentialaly be a problem of your flap popping open. Any surgeon would tell you that this is highly unlikely yet the Navy is still concerned about it.
What I've heard from opthomologists is that although there is more of a chance of complications with PRK, those with LASIK are could be much more severe. For example, an infection forming underneath the flap. In that case you could be in royal trouble.
The reason why LASIK has gained popularity so quickly is because it is virtually painless and results are almost immeditate. However unlike PRK, which is a prococedure that has been done for over 20 years, there are no official long term studies that have been done on LASIK. Not to say that something could/couldn't go wrong in the long term, but nobody knows becasue it is relatively new.
However your comment about procedures being outdated is true. The Navy no longer accepts waivers for RK (blades). Only PRK is eligible for a waiver now.
The procedure is quite simple. They take a laser and reshape your cornea so that you can see properly through it.