About Mushishi - I will preface this by saying that I love the heck out of the show. I actually agree with your point #2. I think Gingko feels like the average person wouldn’t understand mushi or would just be frightened of something they couldn’t see, even if they understood it better. However, I agree with you that he could have at least tried more.

Related to that, I think your fourth point is related to something that I found interesting in that the preventative measures in the setting of Mushishi often took the form of superstition or local myth. Things like don’t cross this mountain after dark or don’t store food in this building that are just common knowledge among the locals, but they don’t really understand why. Well, it turns out that the actual why is often because otherwise you will interact with mushi in a bad way. It reminds me of how religions basically created supernatural origins and explanations for physical phenomena that were not understood at the time.

I think your points 1 and 3 are intentional elements of the setting. I think the author just wanted to slowly wander around through this world and take it in. To a large degree, that is all that Gingko is doing through the story. There are some episodes where he is traveling to a place for a stated purpose, but more often than not, he just happens to be passing through for no particular reason that we know of.