I have a 3dr Mk4, but since then, I think the Golf has grown too big to carry off 3 doors. When the Scirocco was launched, it was thought that it would take over 3 door Golf sales. Granted it is only a 4 seater, but then someone buying a 3 door Golf is not as likely to be carrying many rear passengers. As the Golf has moved on, the Scirocco has stood still, which has no doubt put potential customers off.
If there is a up to date Scirocco when the Mk8 Golf arrives, it should easily replace the 3 door Golf.