Hi,
While you're asking about source code repos, this is very closely related to Source Code Disclosure. Zap looks for Source Code Disclosure in a couple of different ways.
1) Passively, by looking at the responses, and matching against signatures for different programming languages.
2) Actively, at URL level, using the Git / SVN Source Code Disclosure scanners (as well as a couple of other techniques such as WEB-INF information disclosure, and Java class file decompilation).
There is also the Git and SVN options in the Spider, which causes the spider to spider through all the URLs noted in the Git/SVN metadata.
The presence of a Source Code disclosure vulnerability with either SVN or Git, or the fact that the Spider has spidered the SVN/Git metadata means that either a working copy, a pristine copy, or a repo is present. For the purposes of Source Code Disclosure, it doesn't really matter which. Do you need more information on what precisely has been found, or what is it that you feel is missing in this case? Or perhaps you haven't been using these active scanners at all? Can you clarify?
Bazaar, CVS, Mercurial, and repo types other than Git or SVN are currently not supported in any form in Zap (or other scanners, to my knowledge). It's possible, of course, but it's down to effort. Some of the repo types (Git being a prime example) require a lot of low level manipulation and parsing (at the bit level) to parse the repo metadata and various (versioned) data formats, so the development effort is not trivial (understatement). These other repo types are also a lot less common than the more modern systems such as Git, so the cost/benefit tradeoff just means the effort is not worth it.
Having said all of that, if you have any test cases for other repo types that the owning organisation would allow me to test against, I'd be happy to take a look, of course :)