Was there any in game reason to get or want to get now the disk version of a game that is also a cart? Such as Zelda and Metroid?
Only some games were released as both carts and disks in Japan. Zelda was one, but the cart was released very late in the Famicom lifecycle so it's pretty uncommon. If you mean compared to the western carts, I forgot to mention that the FDS also added extra sound channels. So there's different-sounding music in a lot of titles. Other than that it's on a game-by-game basis. Some games might have some extra things that weren't on the cart versions. But mostly it's the same experience, just that you can save your progress and with different-sounding music.
Edit: Main reason to get the FDS is for the exclusives like SMB2j, Murasame Castle and others.