Here's a post made by Thomas concerning this issue:
"I'm familiar with this problem. Been asking about it for years, everytime someone mentions the Black Spot problem with cleaner shrimp. Finally it was Bang Guy who id-it for me.
It is an Epicaridean isopod. This is a parasite that shows up as an irregularly formed black mass in the abdominal region of the shrimp. So far I'm guessing that about 95% of the shrimp that are found to have this parisite wind up dead.
You may find that when your shrimp molts that these black spots disappear, but in many that I have spoken to they wind up coming back, the parisite does not go away."
However, this may not be what's causing the spots on your shrimp. You may want to check your iodine levels and see where they're at. It might not hurt to check your other levels as well.
-lefty