I have polyembryonic Jaffa Shamouti orange germinated. Is there a way to tell which seedling of them is true-to-seed and which is not?

Snu,
I believe one way is to simply observe the leaves closely and look for similarities/differences with the mother's leaves.

Sometimes the other seedlings will die off due to competition. The earlier you can detect the differences as Gene suggests, the better to select the true hybrid.

I bought the fruit from a store, so I have no idea what the mother was like.

Maybe I should just let the seedlings fight it out and select the strongest? Or are there any other ideas?

It depends on how many citrus plants you want-- you could divide them and have 2 plants. If you have access to budwood you could graft one or both in a couple years. You could even graft them, but leave part of the seedling to grow until it fruits which will likely be 8-10 yrs or longer if container grown. Meanwhile it you put mature wood on -- you could get fruit is just a few years. That is probably what most citriholics would do.

Two of the seeds seem to produce only one seedling. If those are mono, that means those will come true-to-seed?