It is very hard to justify building a Harbor but not a Commercial Hub. A Commercial Hub can easily get +3 from adjacency (2 from river, 1 from being in a triangle with the city center and another district). A Harbor will struggle to get more than 2 (1 or 2 resources and maybe a triangle). Often lining up the Harbor with the Commercial Hub for +2 is more important than maximizing the Harbor's adjacency.
The Harbor's buildings are marginal. The Lighthouse costs more than a Granary or Watermill for less housing or worse yields. And all it has going for it is Great Admiral points, which has negligible value if not going for water domination. The Shipyard is crippled by the poor adjacency bonuses on the Harbor. You could run the Harbor adjacency policy, but that is almost certainly going to provide less than the Commerce adjacency policy (and if you want to just run both than you're sacrificing your victory district's policies which are way more important).
The power of Harbors is that they are a weaker second version of a Commerce Hub. Their buildings won't provide all the Gold a Commerce Hub can but their Trade Route and adjacency boost make Policies like "+100% Commerce Hub adjacency" and "+yield from Trade Routes" better.