I've done that ride many times. Some sections have moderate traffic, but nothing to worry about. I did the ride the first time at 13 or 14, so a 16 year can do it. There is a section that you need to ride on the freeway or through camp Pendleton. Can a 16 year old ride the base alone, call and check. Do not ride the freeway. 90 miles is a serious distance I would advise you to find someone to ride with, just makes it more fun.
Depending on the kid I say yes. To become an Eagle Scout, one of the required merit badges is cycling, which stipulates a preplanned 40 mile ride (albiet not on a highway like you would have to from Orange County to SD). Compared to a 10 year old climbing Mt Aconcagua or a 16 year old solo circumnavigating the world, that's nothing. And Orange County and North County are as about as safe as you get and its not like he's in the middle of nowhere, with either train stops back home or you can literally drive there and pick him up.