I mean most creative professionals would obviously take more cores over clock speed any day of the week. Maybe Apple sees the Mini as a general consumer machine, rather than for Pros and the average Joe would benefit from a faster clock speed rather than quad cores?
You'd be surprised how many Pro apps aren't multi-threaded very well. Most of Lightroom supports two threads (generating Smart Previews is the exception). Many tools in photoshop have yet to be upgraded to support 4 or more threads either.