Square dumbed it down quite a bit for the DS version.

1. The encounter rate is lower. It is possible to get through an entire floor without a battle. On the NES, good luck getting off a floor with less than five.
2. Splitting enemies have a maximum of three at a time on DS. The NES version had a limit of six. (Meaning if there's already six on the screen, they won't split.)
3. The dungeon itself is shorter. I believe it's the same number of floors, but they're smaller.

Really, I was disappointed with this dungeon. It didn't have the same feeling on the DS. On the NES, I could sense being in a scary, uncomfortable dungeon. On DS, I was so comfortable in there that I walked back out after Hecatoncheir to level up, never afraid of getting wiped out.