How to cite a site from the dark web?
Is it OK to cite? Yes.

But... While I recognize that some valuable information can only be obtained from the dark side, it is unfair to air a source’s opinion when the source’s identity and motives are shielded from scrutiny. 

So, describe the anonymous sources as clearly as you can. I totally agree with you: "stating their poor trustworthiness immediately after the citation". And note that not everybody knows that *.onion URLs only work in the Tor browser.

About the URL format, cite as any URL, as Anonymous Physicist recommends. I would also suggest you to create permanent records of the web page. Services like perma.cc might help you, it cannot resolve .onion domains, but you can upload your own archive. Another way can be find here.