Support wires are visible above the submarine Cetacean depending on the angle of view. Also, when the sub surfaces or submerges in the ship's home base, rising bubbles and surface waves reveal the actual size of the supposedly huge vessel.
Mark Harris has gills but they can't be seen anywhere on his body when he is wearing his swim trunks. This was addressed in The New Breed (1995).
It is true that gills are not visible on Mark's body on the exterior. However this is addressed specifically in the pilot episode. When Montgomery's character examines Mark after he is discovered washed up on the beach, she discovered his lungs are more gill than lung.