A couple of weeks ago, Jinja Shinpō ran an editorial about “invisible jinja”. This was not about literally invisible jinja, but rather about the ones that do not show up in any statistics, so most people are not aware of them.
There are about 80,000 jinja in Japan that have legal status as religious corporations. There is a great range of sizes and prosperity here, from single jinja that employ dozens of priests to single priests who look after dozens of jinja. One of the major problems that Jinja Honchō is currently tackling is the number of jinja that have the legal status of a religious corporation, but do not meet the legal conditions, most often because they do not have anyone serving as the head of the corporation. Invisible jinja, however, are the ones that do not have legal corporation status in the first place.
These jinja that might consist of nothing more than a stone, or an image of the dōsojin, kami of the roads, but might have a small sanctuary and torii. They might be found beside roads, or in private gardens, or part of the way up hills, or beside rice fields. Many of them are looked after by local people. For example, near my home there is a stone that enshrines the dosōjin. It is just a cuboid stone, with some depressions in the surface, but people leave offerings in front of it and place bamboo poles with a shimenawa between them in front of it. It used to stand at the edge of a field, but when an old folks’ home was built on the field, the stone was preserved.
Jinja like this are not centrally recorded anywhere, which is why it is impossible to say how many jinja there are dedicated to any particular kami. The strength of particular traditions varies by region, so you cannot even get a good estimate by counting in restricted areas and then extrapolating to the whole country; you would need to do a full survey to find out where you had to look in order to get representative samples. The dōsojin are a very popular dedication for roadside stones, and so probably have thousands of jinja, at least, even though they are, to the best of my knowledge, never the dedication of a “large” jinja, one that is a religious corporation. (They are sometimes identified with Sarutahiko and Amënouzumë, but that is only one possibility.) A lot of the ones with a sanctuary are dedicated to Inari, which is probably why you see numbers like 32,000 for the number of Inari jinja in Japan, but any specific number is essentially made up.
The point of the editorial was that the veneration of these jinja is also an important part of Shinto practice, and priests should, in theory, be concerned to ensure that such jinja in their area of influence are properly cared for. In practice, as the editorial acknowledged, priests do not have time do that, particularly if they have dozens of religious corporations to look after, so it ended up as a call to not forget about them completely.
My impression is that this aspect of Shinto practice is really not well understood. Some introductions to Shinto ignore it completely (I haven’t written about it, really, in my Patreon essays), and very few say much of substance. Even the more academic investigations have little to say. This was, apparently, a known issue back in the pre-War days of State Shinto, when there were serious questions about how they fitted into the system. Those questions no longer matter, of course, but this is still a very interesting aspect of Shinto that I would like to know more about.