Great topic @AstroBob - and a topical one for me; I've recently written a guide (updated - version 2) on the forums which covers many of these issues:
I've found this method to embrace the best of both worlds - you have complete sets (as per DAT files, e.g. for No-Intro sets etc) though also have streamlined playlists showing only the original games.
For example, the root platform shows all the roms, but for my main playlist I use the auto-playlist function to narrow the entire set down to USA (and world) region only and released games only. I then try and use the auto-playlist rules to narrow down the set further by excluding duplicates as much as possible. This is done by setting auto-playlist rules to exclude certain terms found in the version and filepath fields. This highlights a current issue however - you can only exclude 2 terms currently, as the auto-playlist rules don't allow AND or OR qualifiers. So it's impossible to exclude all the duplicates necessary to get a fully clean set. Please include this functionality moving forward!
Using the above method, it's also very easy to update the sets as necessary (using the ROM manager as well as the scan for added/removed ROMs in Launchbox functionality).
I keep all roms in the same folder as otherwise it doesn't work with the ROM manager. I collect aftermarket games as there are DATs for those also (e.g. for platforms covered by No-Intro). I collect some hacks but those are less organised as there aren't DATs. I don't include non-playable games, as there's plenty to keep me busy without doing that!