Does anyone know if it is possible to add a note to an Illustrator project, the way you can with the note tool in Photoshop? Currently, I've created a new layer, and set it to not print, but not super efficient.
Not really. Your current method is as good as any other.
There is no "note" tool or feature within Illustrator.
But you can add some notes via the Attributes Panel. These are pretty hidden in terms of someone else finding them, but you can access object attribute notes via actions and/or scripting.