There will probably always be protozoans in any tank but the intent is to minimize them I think. At least the protocol should minimize the numbers so that there is a chance for the the syngnathids to acclimate themselves better.
The pipe fish available are almost all wild caught as there are very few breeders in the hobby.
As for seahorses, the majority of them while technically have been bred in captivity in net pens or large round cement tanks, but still using ocean water that has been insufficiently treated and filters for the pathogens.
Most of the more experienced hobbyists are saving the true captive bred designation for breeders who either use commercial salts, or, use ocean water that they are properly treating and filtering so that there is less chance of pathogen problems once you buy them.
True captive bred seahorses cost more because it is more expensive to produce them but they give you the best odds of chance of success.
The "TANK RAISED" (net pen or cement tanks) are mostly raised for the Asian medicine trade and a very small portion are siphoned off for the hobby. These will be cheaper and most often smaller and often can't be sexed yet because they are too young. Failure rate is quite high in the first six months to a year if they make it past the first six weeks.
Don't be swayed by seeing posts of "successfully mixed" syngnathid tanks.
First, when you see the pictures or videos, the tank may not still be successful. I see posts that claim success but there are very few that follow up the success with later posts.
After all, how many people like to talk about failure, especially if they have previously claimed success.
Second, the numbers of people who actually are successful in the attempts are VERY low compared to the numbers who have tried it.
Just ask the people on seahorse.org or search for an older post on the topic.
Now, I come to an argumentative point on gut loading meds.
I have studied artemia for well over a decade, and from all documented information I can find, brine shrimp DO NOT TAKE IN fluids other than what is attached to their food particles which is minimal to say the least.
Brine shrimp are considered to be filter feeders, but they don't filter like a clam does and remove food particles from the water that they take in, rather, they capture the food passing through their appendages and pass the food on to their mouth and digestive tract. They are not passing the water through and taking the food out of water that is internal.
I don't know for sure how effective it is as I don't have facilities for proper testing, nor money to pay for it, but I think the only chance you have of successful gut loading of liquid medication is to emulsify the med so that it is particulate when blended in water and the brine can uptake it.
This is what Selco/Selcon does to provide for uptake of the fatty acids in their products.
As we don't have access normally at least, to emulsifiers, I've used egg yolk to mix it with and then blend in water, hoping the emulsion is taken up by the brine.
As a back up, I also blend meds in water with spirulina powder and add Focus to bind the med to the spirulina particles.
I don't know if either work or if one works better than the other, but it's my thought that just adding it to the brine water will not effectively work, in spite of what many advocates claim.
Main Reference:
Click here and scroll down to section 4.0, Artemia