Eric,
My experience says that 16,000 threadfin shad stocked into 13 acres with a good bloom will succeed, especially if fish population is balanced to slightly overcrowded. The only time you SHOULD see shad is immediately after stocking, until the population has established itself with young of the year. By late June to mid-July, you should begin seeing "flashing" in the middle of the lake, a sign that yoy shad are beginning to do what shad do...school and become visibly active. By mid-July, schooling bass should be feeding on the baby shad (which will be about an inch and a half long), followed by larger bass getting in the hunt, below the surface fracas.
My bet is that the shad are still there and even if their numbers are reduced by heavy predation, my bet is they will establish.
Here's how I justify those beliefs. First, let's assume, for argument's sake, 95% mortality. That means only 800 shad survive, out of 16,000. If those fish have the chance to spawn, and the 800 are adults, expect them to lay at least 800-1,000 eggs per female. If we assume 50-50 male/female fish, that means 400 females laying somewhere between 320,000-400,000 eggs. If the hatch is "bad" and you only get 20% survival, that leaves 64,000-80,000 babies which will feed on good plankton, head for open water and grow. Whatever percentage of those fish live 60 days, they will be sexually mature and be able to spawn. By that time, the original fish have spawned again. So, think in exponential terms...like the old story about a penny doubling every day. The first few days don't yield much, but just wait...
The second foundation for my belief is that I have done it enough to have seen this exact scenario time after time.
On the down side, I have stocked a number of lakes with lousy to zero blooms and overcrowded bass with countless numbers of threadfins, only to see them disappear like tootsie roll pops at a kindergarten party.
You can stock a lake like that all day, every day and never establish a shad population.
For shad to thrive, a lake must have reasonable numbers of bass living on a backbone foodchain of balanced bluegill numbers and fertile water.

Teach a man to grow fish...
He can teach to catch fish...