He's got a huge radar on those bombers sending in midcourse updates.
If the bombers are taking evasive action, wouldn't that hamper the issue? Also, they are far slower than the "now-fleeing" F-18s and since they fired the missiles from BVR (around 100 km) they will face a hard time tracking the targets which are escaping range at a speed of 400 m/s, or even full 600 m/s. By that speed, in the ~100 seconds required for the missile to reach target, the planes will make another 60 km. Hell, there's no guarantee for successful intercepts. No back-fired missiles on F-18 means they might not be able to down some pesky Amraams, but some missiles will be shaken off by countermeasures.
Basically, Shep expended a lot of his very modern missiles as standoff munitions not to risk wholesale murder of his fleet, but wholesale murder is still not far behind. If he fired at 100 km or so, there's a good chance the missile will expend it's capacity for terminal intercept .
After ~100 seconds of flight, Shep's bombers will be engaging the same type of missile. Since the F-18s went to evasive action, they won't be able to do good tracking too, but they can have Jamming Homing on, Shep's bombers are full of jammers.
In any case, the F-18 force will score more kills than Shep's bomber force, and ultimately Shep's force will be destroyed after it was broken down.