I received answer from Sixt support Benelux:
Thank you very much for your e-mail to Sixt. Apologies for the time it took to get back to you.
It has been agreed with our bonus partners that special rates do not qualify for miles. These include prepaid reservations, [..], special internet offers, van and truck rentals and long-term rentals. Therefore, no crediting is possible for these rentals.
So because I prepaid the rental, I won't get miles. I asked for proof of this rule - in T&Cs or elsewhere. Let's see what they answer, when they answer.