I've run both a 230 and a 330 in my FTP server/torrent box. The Atom 230 is single core with hyperthreading, which means that it uses the OS's thread management to optimize multi-tasking performance, but at the end of the day, it's still a single core solution. Assuming your app takes advantage of multiple CPU cores, the 330 will be almost twice as fast as the 330. not sure how much performance you really need for a jukebox though. I guess if you had .h264 video and whatnot with ffdshow installed, you could certainly benefit from the extra CPU performance, but you're not getting HD video out of any of them, not by a long shot.
I have no opinion on the mainboards. Back when I bought my atom, they weren't for sale individually, you had to buy them soldered to a board already. not sure if this is still the case. I went with a shuttle X27 (atom 230) and then sold it and bought an X27D (atom 330) as I really needed the multitasking performance that you only get from 2 real cores.
The atoms are great for running super cool and being insanely cheap. if you're using your juke just for music/album art/lyrics, the simple stuff, than either CPU should suffice. The 230 should also probably run cooler since it's only 1 core, but don't quote me on that. i can only take measurements from the 330 machine now, since I don't have the 230 anymore.