Aldiko says they designed their app to store books on "the sd card" but all too many devices simulate an SD card on internal memory. I have two tablets and four smart phones here that all do this. Aldiko has been promising since 2012 to "consider adding" a feature that would allow YOU to choose where the books would be stored. You can still see the posts in their support FAQ.
I encounter posts everywhere of people trying to do this, even to the point of rooting so they can use a symlink.
I can only assume not enough people have asked Aldiko for this directly.
If you care.... you could try doing it here:
https://aldiko.zendesk.com/anonymous_requests/new
While you're at it.... ask for an option for a simple book list in text with no thumbnails. I've got lots of documents without covers.<G>