I think the first filesystems had flat layout (no directories), but also had different file types for a library, an executable, a plaintext file. Then there were filesystems where directories could only list files, not other directories.

The original Macintosh filesystem was flat, used for about two years around the mid-1980s. I don’t think I’ve ever used it, personally.

en.wikipedia.org/wiki/Macintosh_File_System

MFS is called a flat file system because it does not support a hierarchy of directories.

I thought that Apple ProDOS’s file system – late 1970s to early 1980s – was also flat, from memory. It looks like it was at one point, though they added hierarchical support to it later:

en.wikipedia.org/wiki/Apple_ProDOS

ProDOS adds a standard method of accessing ROM-based drivers on expansion cards for disk devices, expands the maximum volume size from about 400 kilobytes to 32 megabytes, introduces support for hierarchical subdirectories (a vital feature for organizing a hard disk’s storage space), and supports RAM disks on machines with 128 KB or more of memory.

Looks like FAT, used by MS-DOS, early 1980s, also started out flat-file, then added hierarchical support:

en.wikipedia.org/wiki/File_Allocation_Table

The BIOS Parameter Block (BPB) was introduced with PC DOS 2.0 as well, and this version also added read-only, archive, volume label, and directory attribute bits for hierarchical sub-directories.[24]