Yes, because it's: a) inefficient b) invites a lot of wrong assumptions about the storage format, e.g. about the underlying grammar, the maximum length of tokens or the possible characters than could occur in the file. c) requires you to solve the same problems over and over again (how to represent nested lists, graphs, binary blobs, escaped special characters, etc) d) encourages authors to roll their own format and not research if there maybe is an existing format that would solve their case.

I agree with you, the other extreme - treat binary files as sort of opaque black boxes that you can only access with specialized tools beloniging to your application - is even worse. But I don't see why we can't reach some middle ground: have a well-documented, open, binary format that encodes a very generic data structure (maybe a graph or a SQLite-style database) and a simple schema language that lets you annotate that data structure. Then you can develop generic tools to view/edit the binary format even though every application can use it in their own way.