For who are in hurry: just copy below block and save it as .reg file, like "disable notification.reg". then open it.
Windows Registry Editor Version 5.00
Open Registry Editor(Regedit.exe)
Go to HKEY_CURRENT_USER\Software\Microsoft\Office\14.0\OneNote\General
and edit value of VersionUpgradeDisplayed to FFFFFFFF.
In the image, I removed other values except VersionUpgradeDisplayed, but actually you may see other values.
This key is applied to current user. So you have to repeat this for each user (if you have).
"VersionUpgradeDisplayed" value seems to store last date displayed upgrade message. To test, change the value to 0 (instead of your value/FFFFFFFF). Open onenote and it displayes upgrade message. Back to registry editor and press refresh(F5). Then you can find the value is changed to positive integer(some number>0).
I'm not sure its format but two things are clear: First, great number means later date. Second, onenote compare it with current date when it runs, and display upgrade meesage if the value is small enough (and update the value after displaying).
So, to disable upgrade message we have to set very big number to this value and FFFFFFFF is max value we can get.