I haven't used GDS so I'm just throwing out some random ideas here.
What does GDS index? Documents? Static Web page (.html files) on your disk?
Those questions are leading... If you can expose the OneNote data as one of the formats that GDS indexes then you will probably be able to get GDS to index it. For example, you could have a cron job that checks your One Note database every X minutes and have it run something (like a powershell script) that writes/exports the One Note data as HTML files to a folder on your hard disk that GDS could then index.
This solution idea sucks on many levels (duplication of data, cron jobs, data only updated every X minutes etc.) but it might work.
Good luck.