I would go with bare bottom over having substrate of any kind for a shrimp breeding tank. Java moss would provide protection and food for the babies. The substrate would only alloy food to decompose would it not?
The added deitrus + bio-film etc that grows on the substrate can add the benefit of becoming an extra food source for shrimps so to speak...
although you are quite right in saying one could go barebottom just as easily for ease of maintence...