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Alright, I found the issue. Even though the book metadata had the language set as German (thus setting the hyphenation rules to German), the html files actually contained the tag xml:lang="en". And because "Respect embedded language tags" was enabled by default, English hyphenation rules were applied. The properly hyphenated words just happened to have their hyphenation correctly guessed.
So, for anyone who has the same problem and finds this post: The easiest solution is just disabling [Typography Rules > Respect embedded language tags]. If you prefer having a properly formatted book or if the book contains multiple languages, you'll need to manually change the language tags in the files.
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