Okay, so if I am reading this right, you chose to use her ability after any effect dice are rolled? This was only a minor issue with bomblets, but with the new bomb, I might decide if or which token to use based on what effects they suffer from the bomb.

Also, if multiple ships are hit by a single bomb, can I wait to see what all affected have happen, then use her ability, or do I have to when the controlling player does each ship?

11 minutes ago, Ravenhull said:

you chose to use her ability after any effect dice are rolled?

Effect of the bomb includes rolling for damage, and suffering any damaged or other effect from that bomb. So assuming you are referring to the new Electro-Proton Bomb, she waits until after that bomb does EVERYTHING it needs to do (be that putting an ion or disarm token on) THen she would trigger and decide what she wants to do.

13 minutes ago, Ravenhull said:

Also, if multiple ships are hit by a single bomb, can I wait to see what all affected have happen

No. Her ability states "after a ship". So while you decide the order in which ships are 'hit' and suffer, each ship fully suffers the effects, Sabine triggers, then you pick the next ship, it suffers the bomb, Sabine triggers, ect.