SOLVED
It is indeed an incompatibility between OpenHAB (built with libjna 3.2.7) and Raspbian (comes with libjna 4.1.0).
After trying to convince OpenHAB not to use the system jna-lib (-Djna.nosys=true) - which did not work (no idea, why not), I removed libjna-java and libjna-jri.
Installing libjna-java_3.2.7-4_armhf.deb (from http://ftp.debian.org/debian/pool/main/libj/libjna-java/) and restarting the GPIO input was initialised properly and changes are reported to OpenHAB.
I am running OpenHAB 1.7.1.
I did try OpenHAB 1.8.0 (#1113) with the above solution (replacing …io.gpio…) but that did not work. There was no error, but the GPIOs were never initialised.
I haven’t tried, but this should work with the OpenHAB version 1.7.1 from the repository as well.