Soups were stored in a flat namespace rather than a hierarchical one, largely because the Newton was designed as a single-user device where each application worked with a single data set. The flat namespace and standard data format encouraged data sharing between applications: it was trivially easy to lookup a name in the address book, for example.
The original Palm OS also used "databases" in a flat namespace rather than a filesystem, and for largely the same reasons. Again, I don't think that flash memory had much to do with it. In fact, when Palm OS started supporting external flash memory cards, they used the FAT filesystem (for compatibility with digital cameras and desktop card readers) rather than porting their existing database format.