There is a fundamental division between types of jinja in Jinja Shinto. There are ujigami jinja, and there are sūkei jinja. An ujigami jinja is supported by the people who live in the area around that jinja, while a sūkei jinja is supported by people who feel a connection to the jinja, no matter where they live.
Historically, almost all jinja were ujigami jinja. Travel was difficult and infrequent, and so the only jinja that could become sūkei jinja were those that supported their own organisation of travelling priests. Those priests connected with adherents across Japan, and sometimes guided them on pilgrimages to the jinja.
This started to shift, I believe, in the Edo period, from the seventeenth century. With mass literacy and the spread of print, it became easier to inform people of a jinja’s existence, and with peace and a maintained system of roads, it became easier to travel to distant jinja. However, things really began to change from the late nineteenth century, with the introduction of railways and mass media.
Today, there is a strong shift towards sūkei jinja, and this is creating large wealth disparities between jinja. A jinja that becomes a popular sūkei jinja may have hundreds of millions of yen in annual income and employ a dozen or more priests, while one that relies on being an ujigami jinja is doing very well indeed if it can afford to employ a single full-time priest. If the area an ujigami jinja serves is depopulated, then it is in even worse straits.
There are two concerns about this in the Shinto community. One is very simple: if this continues, a lot of jinja, quite possibly most, will become non-viable — even those with a surrounding population. The other is more subtle. The connection between an ujigami and the people who live in the area, the ujiko, is believed to be intrinsically important. This means that someone who is very devoted to a sūkei jinja is still not following the ideals of Jinja Shinto if they are not also devoted to their ujigami jinja.
Jinja Honchō does produce material encouraging people to visit their ujigami jinja, and some prefectural Jinjachō have websites where you can look up your ujigami jinja based on your address, but the fact that there are tens of thousands of ujigami jinja across Japan makes it difficult for central bodies to act effectively.
This is also an issue for me, as I work on introducing Shinto to people outside Japan. It is clear that a connection to the kami has to go through a jinja if you are to be part of Jinja Shinto. However, it is arguable that no-one living outside Japan has an ujigami jinja. (There are possible exceptions in Hawai’i.) This means that I have to introduce people to sūkei jinja, and so I am contributing to this problem.
At this point, I still have to build structures making it straightforward for people outside Japan to connect to any jinja at all, and I rely on jinja being interested in order to do that. But I do think about the broader social structure, and how I should be working in that context.