The Notes Search by default will roll up information to the Note level. This means, that is a Note is created against more than one Organisation, the search results will show "..." under the "Note for Organisation" column.
Likewise, if the Note was created against more than one Contact, then the "Note for Contact" column will also show "...".
There is an option in Advanced search criteria on the Note search called "Search Result Behaviour" which has options of "Show one row per Note" and "Show one row per Contact/Organisation Association". Selecting the second option will return all Note - Contact - Organisation associations, so you will see all Notes and each Contact / Organisation it is linked to.