Question is, why did they (or at least one of them) eject so late, and that too over sea ?

They should thank God it was a concrete weapon prototype rather than a conventional warhead...otherwise both the planes' pilots wouldn't have any scope for ejection.

As i remember seeing it on Discovery in 'Destroyed in Seconds'...the bomb was sucked in between the low pressure (rather than going straight down) created between the two jets.

I think he was waiting for the right moment to eject so that he wouldn't be engulfed in flames.

Regards