When the occupation directive of 1945 restored genuine religious freedom, the category lost the reason for its existence, and several of its members left.
Tenrikyo, much the largest, withdrew and eventually stopped classifying itself as Shinto at all; it now presents as a religion in its own right, with its own scripture, its own founder and its own centre at Tenri. Shinto Taiseikyo also withdrew. Oomoto, which the pre-war state had suppressed violently, joined. The federation now holds around twelve groups.
Excluding Tenrikyo, Sect Shinto bodies reported something on the order of two and a half million adherents in 2020, the largest of them Izumo-taishakyo with about 1.27 million. These are institutional returns rather than survey results, and Japanese religious statistics are notoriously inflated by that method, but they at least count formal membership, which is more than the shrine figures do.
The category retains a genuine descriptive use, because the bodies in it really are unlike shrine Shinto in the way the 1882 decision noticed. They have founders whose lives are told, revealed texts, doctrines that can be stated and disputed, congregations that meet, and members who joined. A person is a member of Konkokyo in a sense in which nobody is a member of Shinto.
That the state drew the line for its own reasons does not make the line arbitrary. It makes it a case of a government noticing, for administrative convenience, a distinction that scholars of religion have argued about ever since: between a religion one belongs to and a practice one simply takes part in.