Hey! Always glad to chat about this game :)
1. My players joined did a WHOLE lot of pantomime and bartering with Chum before they got an Academic. I bet yours could do the same with the hermits. I should clarify here though that I meant they could fill empty slots, not leave stuff in Manawa. A lot of the most fun stuff has been off of ridiculous use of random starting items, so I definitely wouldn't let them leave stuff behind. For example the horn, which we played as a bike horn, has now become a key component of Chum leadership and culture after a chance trade in Gen 1. I haven't had to deal with ammo at all though, because my one fisher player got The Deep Queen's Harpoon on Gen 1 and never used their harpoonbow.
2. Yeah, ultimately it comes down to your table. I am fortunate enough to play with good friends, so if something isn't working right I can just talk to them about it and we will change it. Hopefully if you don't like how it's working, you feel comfortable enough to do the same.
3. I have had a bunch of morale rolls come up. For me, I just told them if they wanted to run they had to stick together! Which, unfortunately, is kind of a non-answer to your question. While in a more free-form game I have no issue splitting the party, in something like this with more structured turns and important mapping I did not want to deal with the hassle. I guess if I allowed the party to split up I'd let them split a turn's action into different types. I also might make certain turns take longer though, like 2 turns to explore or give a penalty to forage, given that the whole group isn't executing it together. I'd be curious how it works out if it ends up happening for you!