They are masters of hiding...so the shrimp could be hiding anywhere in your tank.
Side note: I had one shrimp that managed to get into my filter...not sure how because it would have had to crawl against the out flow but whatever it died. My theory is that my Dwarf Puffer drove it to suicide.
I don't know enough about mollies to know if they could have eaten the shrimp. But from what I understand of mollies will try and eat anything that will fit into their mouth.