When Zain disappears, you are supposed to interact with the stack of papers that appeared on his desk, to read the letter that upset him. He'll then appear in the backyard of the house and you can continue the story by talking to him there. Atleast it was like that for me. The guy guarding the backdoor keeps talking about the letter if you talk to him, so this was actually one part of the game where what you were supposed to do was actually properly hinted at and quite nicely.
Overall, I agree with a lot of things in your review. The biggest issue with the game is the lack of direction. I had little idea of what I was supposed to be doing and where. I was told to talk to some people, but with little indication as to where those people were and what they looked like. I think it's a mistake to start out the player on the road in an almost empty forest map, you should start at Zain's... cottage? Not sure what it is and then work your way from there, so that you are actually aware this area exists and you can return there, especially since you are required to return there for quests multiple times.
As for the city, well, bonus points for making it feel like a city. The size of the maps only accentuates the issue with the lack of direction though. I'd atleast block off parts of the town until they become relevant. Like, when you try to go to the middle-class area from the Slums without talking to Ralpho, Chase says something like "I should check on Ralpho first, he should be somewhere in the Slums" and you can't progress until you've talked to him. Or maybe just block off the rich district until it actually becomes relevant. I spent half an hour wandering everywhere I could, looking for plot by talking to every NPC and entering every building I could.
I really like the story here btw. It is pretty interesting so far. And the mapping is honestly pretty decent, especially for a first game. The dev certainly has potential.