Why were the space shuttle’s flight controls only certified for low airspeeds?
From what I understand the limits seem to be related to contingency maneuvers such as RTLS or TAL where the external tank was still attached. These were only possible after the solid rocket boosters had been jettisoned, but while the external tank was still attached.

I couldn't find any altitude references for RTLS, but according to this 
TAL required the shuttle to fly to around 350.000 feet. RTLS would have been at a lower altitude and required a 180 degree turnaround. Doing these maneuvers with the ET places a higher stress on the vehicle resulting in black zones. Wayne Hale also mentions this in an old blog post, but doesn't go into specifics.