Yes, notes will stay. Nothing will be changed except for adding the installer. Now if you want to get rid of a jailbreak you have to (or I should say you "should do a restore from scratch") do a restore from scratch, in which you would lose your notes.
it probably will be downgraded, that is if you unlock it. Though this doesn't matter anymore sincer there is BootNeuter which allows you to change your bootloader back if it was downgraded, so as to let you send it back to apple.