Of course there are direct security implications for anything running Flash, meaning malware could begin to target the iOS. While this means that you may be able to run Flash within an app on your iPhone or iPad, the [security minded] good news is that Apple's restriction on web-based Flash content is still in effect as this response from Adobe indicates:
This is great news for developers and we're hearing from our developer community that Packager apps are already being approved for the App Store. We do want to point out that Apple's restriction on Flash content running in the browser on iOS devices remains in place.
Apple's announcement today that it has lifted restrictions on its third-party developer guidelines has direct implications for Adobe's Packager for iPhone, a feature in the Flash Professional CS5 authoring tool. This feature was created to enable Flash developers to quickly and easily deliver applications for iOS devices. The feature is available for developers to use today in Flash Professional CS5, and we will now resume development work on this feature for future releases.