It will be interesting what happens with JD. My oldest is doing it this year - also 16 (although he will compete as a 17 year old due to an end of spring birthday, so ? not your son's group). Our gym owner was just looking at the boys meets with me to see which ones would offer the JD division and happily there are 3-4 that will, and we are a small state, so sounds like there will be enough kids doing it to make a go.
Not sure how a kid with your son's level of skill will match up - here JD seems to be mostly kids who would have been levels 8-9 but are now considered too old with the new rules... or teens who can no longer dedicate enough time to gym to be able to do L10 but don't want to be done. most of whom were late starters, but not as late as your son. With time I hope that it will open up to more kids like yours.
Honestly, I have no idea what JD routines even HAVE to include (as far as number of skills) but putting together routines with enough skills might be the hard part for your son. Vault might have a fair number of boys still doing FHS or Yami...so if he can learn to get over the vault by then it might go...but it will also include kids like my son who will do a Tsuk Layout...or even a Tsuk double...so the variability could be quite huge. So it would be a choice between competing with his skill group but being the older "role model" or competing with his age group but limited events or expecting to struggle. Different kids are more comfortable with those options.
I will say that at 16 if your son really works hard and has good coaches then in the areas he's most skilled at he may make huge gains over the next few months...on the other hand, if he wants to stay in gym a few more years, nothing wrong with competing the bare minimum required by the gym, at whatever level, and concentrating on training for next year - there are always a couple of older L5-7s at meets and the L5 skills are pretty fundamental for the next stuff - DS spent 3 years there then jumped up rather quickly to L7 then L8...
DS is concentrating on staying fit and being a role model for the younger boys, maybe gaining a few skills in his "easy" events this year, and that approach for your DS, whatever he competes, might make meets more valuable.