I think, the 3.3 kernel should ALWAYS return some string, when $node.url_alias is called in a template. Depending on some setting (Probably "URLTranslation"), this will be a "nice URL" or some content/view/xxx stuff. Returning an empty string seems to be a bug.
There is a table for the URL Aliases... is that empty?
Did you use URLTranslations before the upgrade? You could try to DISABLE the URLTranslation in the .inis, so the kernel should return /content/view/xxx URLs, which should get you going again.
Other hints:
- Check the Update SQLs (but i guess, you ran them) - Check the upgrade folder. There are some .phps, that are commonly needed for upgrading... I think, there was one about the URL aliases, maybe this would fill up your DB table with the necessary data.