There is one major advantage of using add on cards for storing books, and that is in case the device has problems with some of the newly added books. If you use a card you keep your devices internal memory clean.
Sometimes it happens that you have a faulty ebook, or a half-written one, that confuses the ebook-reader. It is not always possible for the ebook-reader to ignore or delete such files, which means you need to delete them using a PC connection. Because of the confusion, the ebook-reader might not be able to allow even that, which requires restarting or even reinitialisation of your reading device.
I have had this happen on my SONY PRS-700, as well as my BookEen. The latter prompted me:
An error occurred.
Pleas plug the device
to you computer via USB
to remove recently added files,
or press a key to retry.
(retrying did not help).
Storing books on removable media allows you to remove the card, remove any added—faulty—files using a card reader that is not confused by any ebook internal problems, and have a working device without restarting or reinitialisation.
Another, minor, advantage of using cards can be, that if you use an USB 3.0 card-reader for writing, you will probably have faster writing speeds than can be achieved via a wired connection via the ebook-reader (often USB 2). Given the small size of text only ebooks, this might not be notable too much unless you re-write your whole library.