Players are not drafted based upon their accomplishments. Players are drafted because a scout(s) has concluded that a player has a ceiling which will get him to MLB (assuming all stars line up).
Now, if a player has years of steady spectacular results against competition which has pro potential (in the eyes of a scout), that is often a proxy scouts use in evaluating a player. So guys like Joey Denato (barely 5' 10" in cleats; utterly dominant against tough top end batters for all four years) and Keegan Yuhl (late round 2014 Houston; barely 5' 10" dominant for all four years) get their shots as seniors. (And, both guys continue that domination in MILB so far).
Area scouts will give out FAR more questionnaires then there are draft spots. A player who is not a pick which needs a cross checker (or above) to evaluate, has only his area scout to advocate for the player come draft meeting time. The area scout has only so much influence when advocating against other area scouts.
By the bare numbers - sitting 88-9 - the player fits the mold of a senior sign. Doesn't matter the size. While LHPs sitting 88-9 in college are above average, i don't think that's true in proball. Even a guy like Denato who sat maybe 87 in college, now sits roughly 89-90 as a reliever. So it's an uphill battle for the area scout to get a club to use a pick on a LHP RP AS A JUNIOR. There may be exceptions, but that's just the black box of the draft.
(yes, the player could sign as a FA. Mike Ford signed as a FA junior following an incredible four week stint at the Cape in 2013.)
FWIW, here is my layman advice: work hard, don't look back at this draft (except to use it as motivation to continue to get better), if there is a way to earn a spot in the rotation, so much the better (unless he is a closer); perform well during the summer, have a great scout day in the fall and follow that momentum into the spring, get more credits (enough to graduate would be the cherry on the cake), work on the velo (showing an occasional 93 is better than 91 - it demonstrates that the arm has 93 potential).
Assuming no injury, character issues, and the same type of season, your son will have his opportunity to play proball. Once in proball, everyone has the opportunity to climb the pyramid.
(IMO, the academic achievement issue isn't a factor. Top end players from academic schools are drafted - and signed as juniors - in every draft. Once you get out of the top ten rounds, there is no risk to a club in drafting and not signing a player.)