It was particularly compelling back then when saving a buffer to a temporary file in worst case could involve swapping floppies, but I've always liked the elegance of being able to call external tools and let them read the buffer directly.
I'd imagine the major con in general is that if you want to use it to actually operate on the data, lots of files is slow (open, read/write/seek, close cycle involves many context switches), but making structured data accessible as few files means structured files and potentially complicated locking - the FrexxEd example above is close to the ideal case in terms of simplicity of exporting the data in an efficient way.