They didn't tell ATC when they were aborting (and certainly didn't need to) so we can only make guesses as to when they noticed the hazard.
I think you mean they didn't tell ATC when the
y began the abort because I clearly heard the F.O. on the tape say "bluestreak 390 rejecting eighteen left".
He did this exactly as he was supposed to and he
did need to because PSA procedure requires ATC to be advised of a reject, but not until the aircraft is below sixty knots.
Procedures like rejected takeoffs are well scripted and practiced during airline training.
We know from the tapes that the local controller lost situational awareness and did not follow procedure.
IMHO the pilot of N409DR also demonstrated poor situational awareness and procedure.
He was on the frequency when bluestreak was cleared for takeoff.
He also did not question the controller when she gave him position and hold without stating the intersection
[A glaring omission] and he did not clear the runway before entering it.
The A.I.M. states that pilots departing from an intersection should state their position on the airport when contacting the tower. [AIM 4-3-10]
Even though the tower called him first he could have complied with the intent of the procedure by correcting her.
Here's the NTSB report
http://www.ntsb.gov/Dockets/Aviation/OPS09IA005AB/424166.pdf