The stats are irrelevant because of all of the factors mentioned here (unreliability, padding, etc), but also for more important reasons. Stats are as much a function of the competition as anything. High school players across a wide geographic area (a state, the nation, even a town) play against very disparate competition. Stats cannot tell the story. Stats can't tell if a player is hitting the ball hard or pitching with great velocity. Even when listed on a college form, they are all but meaningless.
What the coach of any credible and respected program wants is first-hand observation and recommendations from respected baseball people. You can learn it here or learn it later for yourself, but high school stats WILL NOT determine your son's baseball future. You (and anyone else) will save yourself a lot of grief if you just set it aside. If your son has real talent, the opportunities will come and at the appropriate level (but even then, nothing is guaranteed).
One last thing, one of the quickest way a parent can alienate a son from his teammates is with their own "personal" stats that they make sure to get out there.