Yes, seahorses can normally tolerate malachite green at the usual therapeutic doses, and Nitrofuracin Green is a good medication for seahorses with skin problems or mild bacterial infections (your seahorses with the "flakies" probably fall in that category). The Nitrofuracin Green also has some antiprotozoal properties, which can be helpful when treating protozoan parasites, as indicated below:
A special formula of two nitrofuran antibiotics (nitrofurazone and furazolidone) + methylene blue and sodium chloride.
USE: anti-microbial, anti-protozoan, antibacterial, and anti-fungal. Wide spectrum. Good for newly arrived fish in quarantine situations. Also be good for healing wounds and ammonia burns on newly arriving fish. Widely used for shipping or packing water. Works well for sores on fish in Koi ponds.
DOSAGE: add 1/4 teaspoon per 20 gallons every 24 hours, with a 25% water change before each daily treatment. Treat for 10 days.
If those are the medication available to you, mermaid, I would set up a hospital tank with freshly mixed saltwater, give your seahorses a quick freshwater dip to provide them with quick relief from the ectoparasites, and then treat them in your hospital tank with the Nitrofuracin Green for 10 days while you are eradicating the mini jellyfish (the mobile medusa stage of hydroids) with the nasty stings from your seahorses take. The Nitrofuracin Green is a better choice than malachite green for seahorses with the "flakies," as you describe it.
Here are the instructions for performing a freshwater dip.
A freshwater dip is simply immersing your seahorse in pure, detoxified freshwater that’s been preadjusted to the same temp and pH as the water the seahorse is accustomed to, for a period of at least 10 minutes (Giwojna, Dec. 2003). It doesn’t harm them — seahorses typically tolerate freshwater dips exceptionally well and a 10-minute dip should be perfectly safe. Freshwater dips are effective because marine fish tolerate the immersion in freshwater far better than the external parasites they play host to; the change in osmotic pressure kills or incapacitates such microorganisms within 7-8 minutes (Giwojna, Dec. 2003). A minimum dip, if the fish seems to be doing fine, is therefore 8 minutes. Include some sort of hitching post in the dipping container and shoot for the full 10 minutes with your seahorses (Giwojna, Dec. 2003).
If you will be using tap water for the freshwater dip, be sure to dechlorinate it beforehand. This can be accomplished usually one of the commercial dechlorinators, which typically include sodium thiosulfate and perhaps a chloramine remover as well, or by aerating the tap water for at least 24 hours to dissipate the chlorine (Giwojna, Dec. 2003).
If you dechlorinate the dip water with a sodium thiosulfate product, be sure to use an airstone to aerate it for at least one hour before administering the dip. This is because the sodium thiosulfate depletes the water of oxygen and the dip water must therefore be oxygenated before its suitable for your seahorse(s). Regardless of how you detoxify the freshwater for the dip, it’s important to aerate the water in the dipping container well beforehand to increase the level of dissolved oxygen in the water. Many hobbyists leave the airstone in the dipping container throughout the procedure.
Adjusting the pH of the water in the dipping container so that it matches the pH of the water in the aquarium is a crucial step. Ordinary baking soda (sodium bicarbonate) will suffice for raising the pH of the water. If there is too much of a difference in the pH, there is a possibility the seahorse could go into shock during the dipping procedure. Preadjusting the pH will prevent that from happening. If you will are unsure about your ability to accurately adjust the pH in the dipping container, avoid this procedure altogether or be prepared to monitor the seahorse very carefully or shorten the duration of the tip to no more than about 4 minutes.
Observe the horse closely during the dip. You may see some immediate signs of distress or shock. Sometimes the horse will immediately lie on its side on the bottom. That’s a fairly common reaction — normal and to be expected, rather than a cause for concern, so don’t be alarmed if this happens. Just nudge or tap the seahorse gently with your finger if it lies down on its side. Normally, the seahorse will respond to the slight nudge by righting itself again and calm down for the duration of the dip. However, if it does not respond, stop the treatment.
Most seahorses tolerate the treatment well and experience no problems, but if you see continued signs of distress — twitching, thrashing around etc. — stop the treatment.
After you have completed the dip and returned the seahorses to the aquarium, save the dip water and examine it closely for any sign of parasites. The change in osmotic pressure from saltwater to freshwater will cause ectoparasites to lyse (i.e., swell and burst) or drop off their host after 7-10 minutes, and they will be left behind in the dipping water. Protozoan parasites are microscopic and won’t be visible to the naked eye, but some of the other ectoparasites can be clearly seen. For example, monogenetic trematodes will appear as opaque sesame seeds drifting in the water (Giwojna, Aug. 2003) and nematodes may be visible as tiny hairlike worms 1/16-3/16 of an inch long. Other parasites may appear as tiny dots in the water. Freshwater dips can thus often provide affected seahorses with some immediate relief by ridding them of these irritating pests and can also aid their breathing by flushing out gill parasites.
If you suspect a problem with parasites, the dip should be extended for the full 8-10 minutes if possible for best results.
Here are some suggestions for setting up a makeshift hospital tank, mermaid:
Basic Hospital Tank set up
A bare-bottomed aquarium with plenty of hitching posts will suffice for a hospital ward or Quarantine Tank (QT). Ideally, the hospital tank should have one or more foam filters for biofiltration along with a small external filter, which can easily be removed from the tank during treatment but which can hold activated carbon or polyfilter pads when it’s time to pull the meds out. It’s important for the hospital ward to include enough hitching posts so that the seahorse won’t feel vulnerable or exposed during treatment. Aquarium safe, inert plastic plants or homemade hitching posts fashioned from polypropylene rope or twine that has been unraveled and anchored at one end are excellent for a hospital tank. No aquarium reflector is necessary. Ambient room light will suffice. (Bright lights can breakdown and inactivate certain medications and seahorses are more comfortable and feel more secure under relatively dim lighting.)
So just a bare tank with hitching posts is all you need for your hospital ward. No heater. No reflector. No lights. No substrate. You can even do without the sponge filters or external filter in your case, just adding a couple of airstones to provide surface agitation and oxygenation. That’s it.
In a pinch, a clean 5-gallon plastic bucket (new and unused, NOT an old scrub bucket!) can serve as a makeshift hospital tank. It should be aerated and equipped with hitching posts and perhaps a heater, but nothing else. This makes a useful substitute when the Quarantine Tank is occupied or in use and a seahorse needs treatment.
Stay on top of water quality in the hospital tank/bucket with water changes as often as needed during treatment, and and when you are treating the occupants for a health problem, re-dose with the medication(s) according to directions after each water change
Best of luck eradicating the mini jellyfish and treating your seahorses for the flakies, mermaid!