Visual identity is every visual aspect regarding a brand (n this case Tor). A logo is part of the visual identity, a letterhead, sticker label, and so on. I think that having a consistent look is very important to have your message broadcasted without "noise". A style guide is a document that explain how someone uses the logo and what can and what can't be done with a brand.

I know that Tor have a very distinct look, the onion logo, but starting a big project like this – rebuild the website – could be the perfect time to update the visual identity.

Ex. This is an visual exercise imagining a visual identity for Anonymous (not actually used).

Bests,

-Marck