The flash apk that you got from Nook contains ARM native code and is not supported by YouWave. To support flash we have other plan which we will not disclose at the moment.
Why it is not recognized by the program (icon not shown) is a different issue. When we designed the program, we let it only recognize apps that are launchable. It basically filters out apps that are NOT launchable but installable. Now the restriction seems to be unnecessary. This is another improvement that we should make. Examples for these kind of apps are: font/language packages, plugin packages, system updates, etc.