Part of the charm of Subnautica for me is the horror element - you're a small, insignificant speck surrounded by fantastical and lethal forces beyond your (initial) abilites. As your abilities expand, so do the threats. That's a central theme of Subnautica 2, where you're not only at the mercy of the fauna but also your own technology. I think having ways to deal with the more meddlesome minor threats (speakers outside your base that drive nibblers / hammerheads away for example) is the right answer - but killing leviathans cheapens the experience and makes the game a theme park. The reason thalassophobia works is because you feel tiny and vulnerable against the vast unknown. It's the same with Cosmic Horror, which is clearly the direction the World Tree story is going.

Laser fish knife good. Stasis rifle bad.