Update! I tried many PDFs and K3 highlights them just fine as long as they are
- text based
and
- unprotected
The only reason for my initial frustration is probably related to the fact that the PDF file where i could not highlight was PROTECTED. I am not sure whether PROTECTED is the right word as i am using Dutch version of Adobe Reader. In my case i see (BEVEILIGD) displayed in brackets right after the file name in the titlebar of the Adobe Reader window.
I am not sure what that means, because i can select any part of the original document in the Adobe Reader and copy and paste it.