Seems only that really only certain parts of the extensions are disabled.
From quick and marginally unreliable testing, I'd say that the extension reference is destroyed, but content_scripts were already loaded before this and stored elsewhere (being that they're run as User Scripts), and still, for the most part, work.
This means all toolstrips, background pages, pageactions, and id (meaning, you can't access resources in your extensions directory) are unloaded. But content scripts were loaded elsewhere and aren't effected.

Although the entire reference couldn't have been unloaded, as chrome://extentions/ shows everything.

Not being technical, I think I concur with that explanation.

Looking at the extensions, they are the only two that have just the Javascript and a Manifest file.

Unlike previously where you could just move the extension out of the extensions folder to disable it you now have to use the 'Uninstall' feature, otherwise you get an error message when it is trying to load the extension.

It obviously keeps a connection somewhere ...

Oh yeah I forgot about that, I should amend the Disable feature of my ExtensionManager. x.x

Yeah, that would be good ...