If you encode them with X.264, you could put each episode onto a DVD-9 using the AVCHD format, as it could be played onto any recend BD player, a PC with a BD-ROM, or a PlayStation 3.
Then, as each episode will be around 8GB, you could put the same files "as is" - no need for re-encode - into a BD-25.
About taking out the black borders: if you want to leave the japanese subtitles, just cut the top black bar, and try to cut the bottom part of the bar under the subtitles...