Gunnar writes about dh-make-drupal and says:
Now, I hate having non-Debian-packaged files spilled over my /usr/share partition. Drupal modules want to be installed in /usr/share/drupal5/modules/module_name (or s/5/6/ for Drupal6, to which I have not yet migrated).
Well, there are modules in /usr/share/drupal*/modules (basically the same applies to themes/), but my understanding is, that this place is intented for drupal core modules/themes. For your site modules/themes /etc/drupal/*/sites/foobar/modules can/ought to be used instead. Of course you can symlink to where ever you want.
Additionally there is /etc/drupal/6/sites/all where you can put common/system-wide modules and themes directories that can be used by all Drupal sites. I don’t know whether Drupal5 does support this, but at least Drupal6 can and you will run into trouble when using this method with Debian packages because of #513522.
So, I would recommend not to store packages into /usr/share/drupal*/modules or themes/ but maybe use something like /usr/share/drupal-contrib/*/modules and themes/ and a tool/method to symlink appropriately into /etc/drupal/*/sites/*/modules similar to update-rc.d or such.
Just my 2 ¢… 😉