Considering how incredibly xenophobic countryside japan is, I don't think having more religious minorities is unfortunate by any standardUnfortunately, nowadays, most kami aren't worshipped anymore, except the major ones. You can see shrines for the minor kami got abandoned all over Japan. It is due to Japanese shifting to Buddhism in Heian period. Another reason is Japan's decreasing population and young people leaving the countryside where most minor kami were worshipped leading to no one maintains the tradition. It is sad since Shinto is really interesting.