Re: Missing side quests.
I have managed to successfully obtain some of the side quests that were missing and complete them in a very strange manner. Here are the steps to recreate how I managed to do this, but I do not know if this will causes issues with your game once they have fixed and restored the issue, so I wanted to post in case this helps with those fixes. This was tested with the Fisherman quest line (I am missing the same exact quests as the original OP). I also play with a dedicated partner for the entire game who is our main host, so I do not know if this works for other hosts. This was also done prior to the patch today.
1) Have your friend host the game. Join their session. We have it set to friends only (not sure if this matters or not).
2) Interact with the side quest NPC and open a menu that covers the entire screen etc. the job screen, Kogyoku's store.
3) Have your friend kick you from the session or quit their game.
4) If you did this correctly, you should still be in your menu. Note that I have tried this with several NPCs who only had chat options, and I got kicked during dialogue, so this MUST be with a NPC who puts you in a full-screen menu.
5) Once you exit the menu, you should see several options to obtain side quests. With Nobumitsu, I actually had all 3 requests available.
6) Accept the side quest, the cut scene should play, and then you should get kicked out of the host session. I repeated steps 1-5 until I got all the side quests from Nobu.
7) You should be able to do the side quests in your world with several issues noted. Any side quest that does not spawn the kemono immediately on the map (e.g. a mob after finding a book) may bug out and not spawn the mob at all. I also had it where I killed the target kemono and the quest did not progress.
8) If you manage to successfully finish the quest, you will not be able to report the quest yet. You must join your friend's session, and then you will see a message saying you can now report. I had to report them back in my own session.
Hopefully that helps solve any issues. Note that I was able to complete the side quests completely out of order as I had access to all parts of the questline. I still have the fisherman's quest part 2 undone, but have done all the other ones.
