I use cyclopeeze in my reef tank for target feeding. Actually, it's technically a zooplankton, as they are crustaceans. Regarding the pigments, there are high levels of astaxanthene and canthaxanthene, but how these affect tadpole color, I have no idea.
Regarding your questions, you are right, phytoplankton is algae - usually microscopic algae (mostly unicellular I think). There's a lot of discussion regarding the various sizes of photoplankton in reef forums, some being very small, others being a bit bigger (but still generally microscopic). There are some studies in coral feeding, but none that I know of for dendrobatid tads.
I think the processing of cyclopeeze destroys most potential pathogens, but I doubt there a re any publications supporting this statement.
Sorry if I'm of little help,
tincs, pumilio, zaparo, femoralis, others