I've just come off a project where the client's standard practice is belt-drive fans with VFD's. I was not privy to the rationale for this, but it appears to be economics. It allows an off-the-shelf fan to be installed in a compact space, using a very standard motor, and the VFD provides a soft-start effect that is good for the belts (vs. across-the-line starting). No special technical staff capable of aligning the shafts is required. These are in largely unattended service (one of those "do more with less" situations) and we found the belts to be in pretty sorry shape. They optimize the package around the motor HP, i.e., if they need a 20 HP motor they sheave it so that at 60 Hz it is max'd out.
I am also familiar with the fan-walls used in semiconductor plants, where very high volumes with very high reliability is needed. The fan-walls' big sales point is once again economics, not technical superiority. Many commodity grade small motors are cheaper than a single high-quality, higher HP motor. (Note this is not a direct vs belt-drive issue, belts' rubber dust is unacceptable in such plants).
Personally, I think the choice of belt or direct drive depends on the client's maintenance staff, the attention they will give the equipment, and of course, what the client tells you they value more, first-cost or life-cycle cost. On small, in-ceiling FCU's I would go direct if it were up to me.