I don't know how you're anticipating people using notes, but if notes is to be at all useful, I can imagine people having many note files (just like the new tutorial videos suggest!)
The problem is that these get added to the visual filters menu which will become completely unmanageable.

There are a number of ways this could be combatted:
- Just have a visual filter for notes, and all notes are turned on/off by this filter.
- As above, but add the option within a note to exclude it from visual filters.
- Have a visual filter for each colour note, so users could turn on all yellow, or all blue notes.
It seems to me that the last option is the best, as it gives users more control, but doesn't require any extra settings/complexity.