Supposedly the shuffle has some problems occasionally with non-iTunes/QT encoded AACs. If you run into any problems use DBPowerAmp to go FLAC to WMA lossless, then use iTunes (on Windows) to automatically convert to WMA lossless to AAC.
iTunes/iPod uses tags for display titles, artist, track number, etc. and if you have it keep your iTunes collection 'organized' it will rename your files to correspond to the tags.
Other systems use tags for display only or completely ignores them (or has no real standard for some codecs). It's a bit of the database versus file tree structure. Depending on what you use for FLAC playback, it could use tags or not. You may not even have them in the files (in which case iTunes would populate song title from track, but wouldn't know album or artist name). It's always best to have complete tag info in your files if possible.