well crystals (they come in both red and black varieties) are the more delicate species of the two most common, caridinas and neocaridinias. (Crystals are caridinas, neos are like red cherry shrimp and their variants). You might want to read up on the specific water needs of the species and fine tune your tank to that. The fish will not mind or be harmed by the change and the shrimp will do much better. I am told pH is the most important number but of course you want all the other parameters in good control too.
I think you would have seen some debris, as in actual corpses not just shed shells, if they had been killed or died of poorly-tuned water. I have kept shrimp with a variety of fish and had no problems with attacks. If you had actual predators like sharks or something it would be a different matter but yours sound like peaceable vegetarians.
Therefore I go with the "they're hiding!" vote above. If, alas, these have or do come to an untimely end maybe try neos next time, they are a lot more resilient and not so fussy. But I love shrimp, have 2 tanks with pumpkin orange neos at present. Hope all goes well.