In its effort to improve the performance iOS 4 on the iPhone 3G and second-generation iPod touch—the oldest and not coincidentally slowest devices supported by the new OS—Apple has removed the ability to sync Notes over-the-air for those devices in iOS 4.1.
Geek.com points to an Apple Support Document that confirms the feature is no longer available on the iPhone 3G and iPod touch 2G, and suggests that users who saw their Notes disappear after the update simply re-sync with iTunes, checking the boxes for syncing notes and for replacing the Notes information on the device, to restore their data.
In addition to OTA Notes syncing, TUAW points out that Spotlight no longer searches through MMS messages on the iPhone 3G under iOS 4.1, likely another change made to improve performance on the older model.