Oh that. Guess you guys didn't know.
Japanese eShop doesn't allow you to buy directly using credit cards.
You need to buy the Nintendo "game cards" in denomination of 500/1000/2000/3000/5000/9000 and add value to the Nintendo account.
http://www.play-asia.com/digital_codes/nintendo_eshop/14/711z7
https://www.amazon.co.jp/任天堂-ニンテンドー...&ie=UTF8&qid=1489469557&sr=1-1&keywords=eshop
So the benefit of buying the game download code of Amazon JP is you can spent just the exact amount of the game instead of needing to overcharge your Nintendo account to maybe like 8000 yen just to buy a 7538 yen game.
EDIT: Confirmed all the DLCs for Disgaea 5 in available in game. Just need to go to the Special Content Shop in game and claim. Some of the DLCs will only be unlocked after certain you complete the initial stories.
I pretty sure they do allow me to purchase the exact amount using local cc. =]

Once you exceed the amount of slots, the other software slot will open up. lol