In my ubuntu installation webapps don't integrate in menu indicators: I tried grooveshark, youtube, gmail, facebook no menu integration and no notifications. P.S. I am using ubuntu 13.10 64 bit.
In order to obtain webapp integration, you should insure that you have the proper repositories (universe) enabled and install the unity-webapp-$appName for the package you want to have integrated in the menu. Then visit the site in browser and you will be offered the opportunity to install the webapp from there. There are several in the repositories available to choose from. Do hope that helps.
Have a nice day.
This bug was already pointed out in https://bugs.launchpad.net/ubuntu/+source/unity-webapps-gmail/+bug/1245027.
In order to solve it, you have to install the package available here: https://launchpad.net/~justinmcp/+archive/webapps-ppa. More precisely:
to add ppa:justinmcp/webapps-ppa to your system's Software Sources, open a terminal and enter:
sudo add-apt-repository ppa:justinmcp/webapps-ppa
to pull down the latest list of software from each archive it knows about, including the PPA ppa:justinmcp/webapps-ppa you just added:
sudo apt-get update
It works fine for me (Ubuntu 13.10 Saucy, 64-bit).
See also these questions: GMail not visible in Unity panel, Gmail Webapps and 13.10 - Unity and Message Me Menu Integration