I prefer rack and pannier to rack and trunk bag. As others have noted, panniers offer much more capacity, and allow for shopping/errands. Some panniers (e.g., the Trek grocery models) even fold up when they're not filled so they're more aero.

But the main reason I don't use trunk bags is because they would block my DiNotte 140L tail light. I run both the tail light, and my DiNotte 600L head light, from a single battery that rides in a half water bottle on the seat tube. The 140L is always on (day or night), and mounting it further aft would be a hassle.