Just arrived in Kyoto a day ago, and accepted all the partner quests, like The Mysterious Fly and other stuff, but Shinoda Hell is the only dungeon that isnt open for me yet, how do I unlock it?

And YSD unlocks after completing everything else?
quests like: The Mysterious Fly, Nue and Lady Shizuka, Hashihime in Love, Ibaraki Douji from Rashoumon, A Lost Little Centipede and Wailing from Nishidera?

It unlocks after you do the main quests through to the yellow shire dungeon. (beat benkei) Shinoda will unlock after that.

First you need to clear the partner quests, namely Kaguya's. She finds a paper ghost their that will follow her around. Eventually, after the Spire, this ghost will remove the seal on Shinoda.