1. The biggest advantage of storing on the filesystem is that Files are the core primitive on UNIX based operating systems, and is core-enough on Windows. Giving that up would require tremendously good reasons.

2. Everyone organizes projects into folders differently, but in most languages the only reason why you organize things into folders is to make it easier for humans to find things. The computer doesn't care where the files are stored. So, you're proposing: Give up a feature that exists solely to make it easier for humans to find things; its extremely difficult to envision a world where this results in a more ergonomic world.

3. The hierarchy is only one way of thinking about how you can browse a filesystem. There is nothing stopping editors from indexing files in different ways, allowing you to browse by, for example, files tagged with some comment at the top, or files which contain classes versus interfaces. In fact, more comprehensive IDEs like JetBrains already do this for some languages. You don't have to change the storage substrate to get 100% of the benefits you propose, with the extremely small cost of some indexing process when a project is first opened.

4. There are twenty billion programming languages out there, like four of them do what you're suggesting, yet no one uses any of them for anything meaningful. There is nothing, period, stopping any new language from doing something like this. Golang could have been designed like this; but it wasn't.