I think John started it. Back in the gallery there is a picture of Applejack encountering a sea pony and trying to deny it. Fans liked it so he drew some more sea pony Lyra, then other artists picked up the idea. And Sea Pony Lyra became a part of fandom.
Why are they so underrated? WHY NO LOVE FOR YOU, SEA PONIES? With your awesome shells and ocean-themed accessories, you were the best My Little Pony bath toys because you belonged in the WATER unlike some OTHER ponies.