A lot of time and energy is spent on thinking about how to organize your notes into folders, and many people use Quick Switcher as the main way to both create and open notes, even to simply access some information. I started this way, too.
But none of this is necessary, because Obsidian is a non-relational (NoSQL) database containing information of a data type called graph. You don't access information in a database by navigating to a table and opening it up, you use queries. In Obsidian, you can use filters.
Filters can be bookmarked, and the bookmarks can be organized any way you want. This way you can build an information tree instead of a file tree. You can easily move your information around, and even have the same information in multiple locations. With Hover Preview and Hover Editor, you don't even need to actually open files except when creating or developing them.
I wrote a series of articles describing this system. It seems a bit scary at first, but the efficiency gain is considerable. You can read the articles here:
Website:
Substack:
Medium.com:
There is no one fit all way.
First, structuring you notes in s tree like structures using folders is a valid approach (independent on real files structure).
Second, some people, including me, expect that their notes can live longer that tools, in this case it makes sense to not rely on tool features too much.
This is not for everyone, I agree. I don't see how it ties my notes to any specific tool, however. It doesn't impact the contents of notes. It's just a different way of interacting with them.