Suppose we've colonized a planet with 99% of the surface area covered by oceans. It has submerged continental crusts, averaging 200-500m underwater, with the average depth of open ocean being 1000-1500m. Other than the difference in surface geography, consider the planet generally earthlike (unless deviating from Earth-normal conditions is necessary to answer the question).
Colonization was via slower-than-light generation ship, so this colony must be self-sufficient. Natural resources are mined from the rock of the continental shelf, which requires either above-water mining rigs or seafloor bases at shallowest parts of the ocean.
In the real world, surface ships and installations are far, far easier to build and sustain than their underwater equivalents. They don't need to be sealed against intense pressure and they're less mechanically complex to maintain, even if I posit a non-breathable atmosphere to eliminate the advantage of not needing to be sealed at all. But I'm looking for a reason or reasons to justify this colonial civilization being primarily aquatic, living in submarines and undersea installations exclusively, rather than ships and oversized oil rigs.
The best justification I've been able to come up with is extreme weather on the surface. According to this question/answer, a mere 133m depth is sufficient to ride out the worst storms overhead. However, since oil rigs seem able to survive hurricanes as long as they're built tall enough to avoid the worst of the waves, I'm skeptical that all the headache of an underwater city would be more attractive than just building a more storm-resistant above-water installation.
Simply put: Why live underwater, rather than on the surface of the ocean?