Andrew,
Many do. Even at the top of the new course market, when there were almost 400 courses built, Toro said they were sending out 400 catalogues to gca's. With the top ten gca's doing perhaps half the total new course work, the math means that many, many, gca's somehow survive on remodels, master plans, consultings and perhaps nine hole extensions, alternative courses and the like.
On the few clubs that have paid me a retainer, it's only an up front fee that goes against total hourly services. If they end up wanting more than the normal few times a year consulting, then they have to pay extra hourly charges. Then, for major projects, we negotiate a separate fee.
BTW, it seems to me that master plan fees are rising quite a bit. There was a time when gca's did them about break even as a loss leader to "lock in" the construction phase when something actually happened. Now, we try to make the MP profitable as well, and also provide more services - mostly in the preparation of 3D graphics using CAD and Photoshop. I think that helps, because I doubt most club members could actually read the master plan prints very well and know what they were getting.
While I don't hear the details of too many of these from other gca's, I am getting the sense that the "standard" MP fee is $35-50K these days. I have heard MP fees of as low as $17,500 and as high as $175,000 for a well known architect.