The points per fotos refer only to the alignment step, so they don't have so much relevance for the final model or DEM. And yes, using less points per foto will result in faster processing, in particular in the matching step. In the model building step, this should not really have an influence on processing time and model quality. I always leave it at 40,000, but for large sets of images (many hundred or even thousands) it may be reasonable to reduce the number a bit. If you go too low, I suspect that the risk of false matches and resulting alignment (and perhaps camera calibration) errors would go up. I assume that the Agisoft people have done some testing which led to the preset number.