I concuur with the OP, this is probably going to be THE civilization 6 problem. Not that it wasn't present in previous vainilla civ entries, but this time it would seem that the district system will aggrave it it. And yes, this is a problem, for it turns navies into useless husks.
So here there are some ideas as to how to solve it:
- Grant an extra trade route ONLY to cities placed directly in the coast, rather than to every city with a harbour district
- Make the coastatal housing bonus add up, rather than replace the riverside housing bonus, thus making river mouths prime locations for setting cities (as it happens in the real life)
- Increase sea tile yields, for crap's shake. Make EVERYTHING increase sea tile yields: policies, wonders, buildings... hell in civ 6 the lighthouse doesn't even add food. Oh, and increase ocean base tile yields too, now that we're at it (they should produce 3 food at the very least). As for how to archieve it:
Regular lighthouse: +1 food to sea resources in this city
Harbour: +2 production to workboats in this city
Salt luxury resource: +1 food to sea resources in every city
Refrigeration tech: +1 food to every sea tile in every city
Maritime industries SP: +2 gold to workboats
The colossus: +1 production in every deep ocean tile of your empire
The great lighthouse: +1 gold to every coastatal tile of your empire
The venetial arsenal: X2 to the yields of this city workboats
Gaining suzerain status over Nan Madol city state: +1 culture to every coastatal tile and adjacent district
- Make the possibility of building certain districts in swallow waters or unlock water-building by certain techs. Also: Adjacency bonuses, please (extra amenities for entertainement districts, extra gold for commercial districts, extra production to industrial districts if next to sea resources, special "oceanographic institute" building for science districts...)