Of course you're right, there is no "prohibition" to create your own tables but many plugins (including the one which inspired me for the post) store minimal data in the db and create a totally unnecessary table for it. Additionally they create unnecessary code to organize the data (e.g. connecting it with a posting) instead of using the WP functions. If you're storing data that does not fit into the default scheme or if it's much more efficient it's a good reason to create an extra table. I'm doing it myself in one of my plugins to store logging data.