There may not be much done on anemones but there is plenty of research done on corals and the plot thickens that stressed corals are vulnerable to infections.I think @OrionN has seen what a lot of us have seen that supports the idea that there is a pathogen present with anemones that are demonstrating sick responses. Just introducing a sick anemone to a tank of healthy anemones and observing the resulting failing health of the previously healthy anemones is a direct correlation that supports the pathogen bacteria hypotheses. The same does not typically occur after introducing a treated anemone to a tank full of other healthy anemones.
I know @2Sunny you want a published paper with detailed experimental design and results, but it just doesn't exist yet as far as I know. Just citizen science, which at the moment lends a pretty strong argument toward Ciprofloxacin treatments helping more than it harms. I think we would all love to see a published paper on the topic though! And maybe one day it will be done, until then I'm going to continue treating new nems with cipro because it's the best solution at the moment for me.
As for anemones - If you consider how they are shipped - in a relatively small bag - and that it may take 2 solid days or even more between the moment they are packed at the collection facility and finally unpacked at the importer, it is a miracle that not all arrive sick. Often they sit in their own filth for most of that period.
I think the reason why giganteas are more prone to these infections is that, as animals of the tidal zone, they are used to higher oxygen levels and during shipping they may suffer under oxygen depletion, especially if bacteria blooms occur and consume oxygen as well.
I will definitely continue to treat sick anemones as this has so far - despite a few recent setbacks - worked quite well for me. Even "easy" anemones like BTAs will sometimes need it and I brought a bunch of them back to health with Cipro.
The one antibiotic I would not recommend for anemones is Septra. So far I had not a single success with that one. It is however often a good choice to rescue freshly imported sick anemonefish.