EDIT (2023-07-31T22:18:52Z): I have realized that I was not clear in my original intent for this post – it could be interepereted to mean that I am asking whether or not you could access, for example, Lemmy through the Tor browser. This is not what I meant. What I was more alluding to was if it were possible to create a sort of “hidden fediverse” that was separate from the fediverse over the clearnet. There exitsts, already, Dark Web forums, like Dread, and I wonder if those would benefit more from being federated – Lemmy seems like a good candidate for this.
Title changes: Added “More specifically, could one make a sort of “Hidden Fediverse”?”
Depends on the specific instance. Some services run where they are natively accessible through tor, but most don’t.
Just remember that ActivityPub is a sharing protocol, and individual admins are fully capable of seeing everything. There is no end to end encryption, everything is stored in plain text.