Indexing does not occur twice. The WHS content is indexed on the server and remote queries are sent to the WHS box to return results. Therefore there is no duplication.
If you make such content "Available offline" then the content is synced down to the local machine. In that case, the content is indexed locally.
If you travel outside of the home, then the WHS folders included in your library are 'unavailable' since you are no longer connected to your home network. Once you connect back to the home network, they will be available again.