Mathematics was dispersed across several departments, and this was not a weakness but a strength.
You said "It had a pure mathematics department, an applied mathematics/theoretical physics department, and a department of statistics and somethingorother (maybe economics?)."
That sounds like 3 departments that focus on math.
I think you're right that mathematics is dispersed across several (math) departments, but that seems to miss the point of this change. After dispersing individual Classics faculty across other departments there will be zero departments that focus on the classics.
The point is that it will be hard to collaborate on Classics-focused work. For example, one way that a college/university can increase it's reputation in an area is to organize/run conferences. It'll be that much harder for Classics faculty at Howard to do that because each individual faculty member is now in a department that doesn't focus on the Classics and so won't have much incentive to support work (like organizing conferences).
Does my distinction make sense?
I'm having a hard time reconciling your comments with the distinction I made, above.