@Kerosene Quite a few at different points in time.
http://demo.fedilist.com/instance?onion=only
http://demo.fedilist.com/instance?onion=only&state=down
Most of them are abandoned Mastodon 3.x instances hosted via Start9, some Yunohost-esque panel for easy setup of hidden services. Two outliers of note are rawr onion, a flagship Pleroma instance in the network and Onionket instance which is just Baraag on Mitra.
As for I2P, there's been pubsub.i2p (closed down in January due to inactivity) and iwojima's instance. Don't know if there's been any other ones.