absolutely 100% agree with you, the notes sync is a potential problem for apple if ios9 and El Cap are released separately.
Unless they were to offer an Yosemite notes update.?
It's not an issue. You have the option to upgrade notes to the new format or leave them in the existing format when you start the app. Leave them in the old format and upgrade if/when you install El Capitan on your Macs etc.