There is a constant push and pull between airlines saying the GDS cannot support ancillaries and GDSs saying they can. A more accurate judgment may be that GDSs generally do accommodate ancillaries but in a clunky and limited fashion.
Full-service airlines are increasingly adopting LCC elements, with demands for GDSs to support ancillaries. Even the most steadfast of full-service carriers have some ancillaries, mainly charging for exit row seats (Singapore Airlines) or a seat assignment.
But travel agents may not hold the same vigour as airlines to sell ancillaries. They find using Special Service Requests (SSRs) difficult…they may not have a monetary incentive to sell ancillaries since they typically do not receive a commission on them.
The existence of the middleman (travel agent) is becoming more problematic as airlines slowly grasp the importance of retail psychology: what you sell is as important as how you sell it.