They enabled aircraft to make fuel stops at undeveloped supply caches that happened to have a functioning seaport, but no long runway. This was necessary both because of the scarcity of paved runways at the time, and because the short ranges of the time necessitated multiple fuel stops in order to make long-haul journeys.
Once those necessities faded, both because of the build-out of airstrips worldwide (e.g. paved runways in Sri Lanka) and because of improving aircraft technology (no need to stop in Sumatra on the way from Java to Sri Lanka), there was no reason to go with an aircraft that couldn't land inland and had its aerodynamic properties constrained by the need for seaworthiness.
In the end, it's more practical to deal with the problem of finding an airport (after all, there are a lot of airports) than to solve the other problems of making a large sea plane.
Also read an interview with a pilot that flew Clippers. He said maintence was nightmarish due to salt water. And also being able to land in water sounds good until you factor in weather and the need to eventually dock.
Edit: answering my own question https://aviation.stackexchange.com/questions/24526/has-anyon...
There are still some large sea planes used for fire fighting service and a few airworthy PBY Catalina's.
See
https://en.wikipedia.org/wiki/Canadair_CL-415
and
https://en.wikipedia.org/wiki/Consolidated_PBY_Catalina
Catalina's were heavily used in WWII for scouting and rescue in the Pacific. There is a partial documentary of some guys flying a Catalina around the world which was cut short when they were forced to abandon it in Saudi Arabia.
https://www.qantas.com/travel/airlines/history-catalinas/glo...
> The flying boats, travelling at about 200km/h, would take an average of 28 hours to complete the journey, but up to 32 hours nine minutes when winds were unfavorable.
Description of flying those was, they were docile but didn't have power assisted controls. Flying one for 30 hours in shifts even must have been brutal.
The development of a system of airports (+ new planes that could fly trans-oceanic flights without stop-overs in far-flung locations).