This was probably because of an dying microSD Card where the kernel was installed. Because 2 months later also the 4.9.0-13 kernel on hold had boot problems. [1] After reinstalling Debian Stretch with 4.9.0-14 on an SSD instead of microSD (except u-boot) everything runs fine. [1] https://www.olimex.com/forum/index.php?topic=8028.0
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