I've used prazi in a cycled QT tank without much of a disruption, but it did definitely put a significant dent in the populations of amphipods, mysis, and bristleworms. It may not be something that the reef keepers are even noticing, and if it works without adding too much ammonia from die-off to your tank, then super. I do not think that it sticks around the way fenbendazole/panacur does, to continue killing off inverts for practically the life of the tank, so it isn't as critical that you don't use it in the display. I am inclined to believe that it isn't selectively killing off the worms, and instead, your fish are not ending up quite as "de-wormed" as you were hoping.
I still feel that if you want to effectively treat internal parasites in the gut (or for that matter, those that have migrated from the gut to other organs like the swim bladder, liver, etc. during their larval stage), you are not giving yourselves the best chance by using a bath. I'm sure it is at least a little effective, since some is metabolized when the water passes through the gills, etc. but personally, I feel a lot more confident making sure my fish ingests a medication (or is injected with it) when trying to treat for an internal problem, provided that is an option to me. Delivery method always makes a difference. Deworming your pipefish wouldn't be a bad idea anyway, and it really is not very hard to gutload praziquantel into adult brine shrimp to feed to the fish. You only need to do it one day a week for 3 weeks (feeding two meals in that day, 12 hours apart), so it's not that involved a process either. And, as long as you are just gutloading adult brine shrimp, and you have some on hand, you can do a round of metronidazole/flagyl after you are done with the prazi, and then
really feel confident that you've targeted the majority of the types of internal parasites your fish might be carrying.
