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.
In regards to your first question, it is absolutely fine to cite anonymously published content. This is just a special case of citing a primary source. Primary sources often suffer from issues from trustworthiness, bias, and verifiability and they are routinely cited.
Anytime primary sources are cited, it is the authors' responsibility to provide sufficient context for readers to effectively evaluate the source. You might do this by explaining that the authors are anonymous and you cannot verify the veracity of any of the claims. You might even point out that there is evidence that the claims might be false. As long as it is framed responsibly, you should be fine.
In terms of your second question, I don't think there is any style guide that will help. In these case, I would just focus on the fact the goal is to allow people to easily and unambiguously identify exactly the page that you are referring to. There are a few approaches that I think will accomplish this goal. Providing a .onion address with a note like "(Tor hidden service)" might be enough to help people identify how to access because they might then look on the web for how to access this.
That said, since the .onion URLs — like all URLs — are likely to disappear, I think a better idea would be to use a perma.cc archived link of a Tor2web proxied URL. Tor2web proxies do not protect the anonymity of readers and are, themselves, not entirely stable. That said, for the purposes of creating an archival copy of a citation, they will be entirely sufficient.
Ideally, in the most strict sense of the word we should cite only material reviewed by professionals who have no conflict of interest with the authors, and this material better be published in a reputable journal. That's how we try to ensure trustworthiness. However, Web content is mostly not reviewed, and we wish to cite it, since there is some useful data over there. But there is also a lot of junk in the Web, and the presence of the author's name or nickname John Doe sometimes adds nothing to the trustworthiness. (Even professional agencies like Reuters, AP, or TASS sometimes produce junk which later goes to the websites of newspapers.)
That's a hole in the publication process: reviewers do accept papers citing low-quality websites, and the Tor sites are not an exception; simply the author of such sites is unknown. In terms of trustworthiness, all the following signatures are completely equivalent:
[no signature]
nickname like Sally6pack
pseudonym like Fred E. Ricks
unknown person like Max Müller
very well-known person like Bill Gates but on an unknown third-party website.
Whether you use this hole (and if so, how) or not is your own, personal, ethical decision.
(If you care: my own, purely subjective take on it would be that stating the poor trustworthiness of a website immediately after/before the citation or in the bibliography is fine.)
As for bibtex, use the note field to provide any information of how to access the material. You might alternatively consider biber+biblatex and use @online. I would refer to a different website with a HOWTO regarding accessing .onion.