The human body,
My first exposure to science fiction stories set under the ocean was Twenty-Thousand Leagues Under the Sea. My apprehension was fostered by CBC Theatre 10:30's excellent adaptation of John Wyndham's The Kraken Wakes (Out of the Deeps). My fascination, however, began with a 3-part Worlds of If serial published in 1967 by Hal Clement. Ocean On Top was later released in 1973 as an early DAW paperback with a great Jack Gaughn cover.
Why the fascination? Apparently, I'm not alone. An internet search of undersea science fiction leads to many sites and lists. The covers sell it (or art-Frank Tinsley lovingly portrayed all kinds of future habitats in many speculative articles for Mechanix Illustrated); the words embellish it. Whether it be sleek submarines hovering over domed cities under the waves, or surgically-altered gillhumans riding sharks (Kenneth Bulmer), the images are compelling. The sea floor is the unknown. Humans at best interact with the epipelagic photic zone on a regular basis. The abyss beckons and threatens. It's dark and cold; fatal to humans outside a pressure-protected environment. The lure of being able to interact tactilely with whatever denizens of the deep may exist is strong to the exploration-minded. A truly alien environment.
Alien environments are great settings for science fiction exploration. Extra-terrestrial survival requires similar gear to undersea survival: suits to contain and protect the fragile human form. Yet there is a fundamental difference despite the morphologic parallel. Survival in outer space requires keeping the earth's environment inside the suit or living quarters. Establishing an outpost in the depths of earth's oceans requires keeping that environment at bay. Surviving under immense pressure may still be easier than in a radiation-charged vacuum.
Every generation of writers returns to the water. Fred Pohl and Jack Williamson's YA classic Undersea trilogy has been re-issued many times. Kenneth Bulmer did his take with City Under the Sea and To Sail the Silver Sky. Frank Herbert's Under Pressure is another 1950's vision. Michael Crichton's Sphere brought the subgenre (or submarine genre) into the 1980's and Peter Watts drove a spike into its heart with his disturbingly brilliant Rifters saga at the close of the 20th century.
To return to the question of relevance, science fiction is often a cautionary tale forum. Ecology and overpopulation were brought into the SF readers' consciousness by such authors as Ursula Leguin (The Word for World is Forest), Harry Harrison (Make Room! Make Room!) and John Brunner (Stand On Zanzibar). The oceans can be as fragile as terrestrial ecological systems so the literary opportunity to examine issues, options and solutions is very relevant to 21st century life. Overpopulation isn't going away and the oceans feed those nations who can afford to harvest from the sea.
I suspect I've missed some recent SF undersea novels and that the genre is alive and thriving. I hope so.