When treating for ammonia poisoning or nitrite toxicity, which leads to respiratory distress by converting hemoglobin in the bloodstream into methhemoglobin, a form that cannot pick up and transport oxygen, methylene blue normally produces very quick results. In most cases, the seahorses will fully recover none the worse for wear within 24 hours, even in severe cases where the oxygen-deprived seahorses were so weakened that they had to lay prone on the bottom for extended periods of time, unable even to right themselves much less cling to a convenient hitching post or swim.
If the methylene blue does not provide your juveniles with quick relief, then I would suspect that the symptoms you have noticed are due to something other than a spike in the ammonia or nitrite levels in the aquarium. For instance, the symptoms you describe, such as tail whipping, lethargy, respiratory distress, using their tails to scratch their heads, and loss of appetite can also be caused as a result of the irritation from protozoan parasites.
If you suspect a problem with protists, then the appropriate treatment would be to add a small dose of formalin to the nursery tank or rearing tanks every other day. Juveniles and seahorse fry can tolerate low levels of formalin without any problem, and many home breeders will use it in there nursery tanks in order to keep protozoan parasites and bacterial blooms under control. The recommended dosage for this purpose is to add 1-2 drops of formalin per gallon every other day.
Just continue to add 1-2 drops of formalin per gallon every other day. Dose the tank with formalin one day, and none of the formalin the next day, and then re-dose the tank on the following day, regardless of the small daily water changes. (Just wait several hours after you add the formalin before you perform the next water change.) You can maintain these prophylactic treatments with formalin in the nersery and growout tanks tanks indefinitely, so you can keep it up as long as you feel it’s helpful.
However, you’ll need to beware that formalin basically consumes oxygen, so it’s very important to keep the juveniles’ tanks well aerated if you will be treating them with formalin prophylactically. Maintaining good aeration for at least several hours before and after you add the formalin.
Best of luck resolving this issue and getting your juveniles back to normal again, Matt.