I'm developing a PyGTK-HTML5 Application (Using Quickly), but the webkit libraries (WebView) are a bit old, at least for using some of the latest HTML5 APIs (like IndexedDB) is it possible to upgrade the libraries? and if so, when I package the app, will it have that specific library that I just upgraded?
Yes it's possible.
No it's probably not worth it for redistribution.
If you did manually update your pygi+webkit you would have to shove that in a ppa and depend on your own packaged version of WebKit in order to "send" the functionality to other users.
You would run the risk of breaking other things that depend on the current version in repo, which is why there is a version freeze on distribution release.