Yes you can use DL DVD's... that's what the nav disks are. And yes, you can use a folder system on the disk to sort everything, you just have to burn it as a data disk.
As far as DVD changers go, I'm not really sure. Try doing a search for "dvd changer" on the D-series forum. I know somebody's asked about that before on a few occasions. But if I recall correctly, since the D3 doesn't have an AV-BUS input, you can't control an external hard drive. I would suggest either maybe putting all your videos on an older 5th gen ipod and hooking tha up, or maybe even buying a HDD player, filling that up with your videos and hooking that up to the rear AV inputs.
HDD player: http://search.ebay.com/hdd-video-player_W0QQfkrZ1QQfnuZ1QQfsooZ2QQfsopZ32QQkeywordZhddQ20videoQ20player
You just buy one of those, throw a hard drive in it, load it up with music and movies, and attach it to the D3's AV inputs. You control everything using on the D3's screen using a remote control. Mush better and MUCH less expensive than a DVD changer.