Within YA mysteries, my favorites as a child were The Three Investigators. They had more clever plots than the Hardy Boys and other series, and the protagonists did more actual deduction, observation and reasoning. Also, cameo appearances by Alfred Hitchcock! Sadly, they don't seem to be available for Kindle.

If she hasn't read it yet, you could give her Sherlock Holmes. Quite a lot of (19th century, but still) science and methodic reasoning, should be read before other classical mystery authors like Agatha Christie (because all were reacting to it), and with the bonus (for you) of it being out of copyright and so free for Kindle.

As for SF, how about Jules Verne? It is different enough from current day SF that if she might like it even if she has a prejudice against the latter (no spaceships, aliens, rayguns, etc), but teaches a deeper appreciation for science and scientific progress than most modern SF.