Probably, baseball wise it might not make a difference. The lone factor that occurs to me is the high school baseball experience does provide a standard/baseline applicable to all other high schoolers. There are factors in HS ball like leadership, dealing with bad coaches, players you don't like etc. that aren't always as evident, IMHO, in select ball. In select ball when you encounter something you don't like you try to change it or quit.
Also, select teams, though this is a generalization, tend to coddle kids because of the investment aspect of time as well as money so PT may be more guaranteed. Parents have a say in pay for play select teams...HS NOT SO. In HS coach doesn't have to answer to parent...they may but don't have to. You and your son need to experience this...because in College ball that coach doesn't care what parent says unless that parent is a HUGE "donator/alumn etc. to the school.
That said, consider the socialization factor as well. Say what you will, the trials, tribulations, and imperfections of HS parallel those in life because as citizens in a large population, or HS students, or College students there are rules and regs that have to be dealt with and they are not all written down.
Tempatations you may worry about in HS are even (IMHO) more tempting in College where Mom and Dad aren't there to "keep an eye" on you.
Bottom line, to me it's better to throw them in the shallow end of the pool to see/teach them if they can swim (HS while your still with them and can help with some tough lessons), than the deep end (college) when they are all alone and have no one to throw them a life line.