I realised that when importing xlsx-files in which data ranges are defined the import of the xlsx-file will not work via WebDirect. Using the client will trigger an extra window where you can specify if you want to import the entire sheet or separate defined ranges. This appears to be exactly the step where WebDirect jumps off. As soon as I get rid of data ranges, thee import works as expected.
I haven't found any related observation so far and was wondering whether someone has ever experienced the same issue and found a fancy workaround. WebDirect should at the minimum be able to ignore the defined ranges by default. Otherwise I need to tell a lot of my clients one more thing that they need to take of before importing data.