Target acquisition: this again tricky - if it is affected by chaffs, and scans not, so would it not make sense to use the scans to lock on a target (since it is not affected at all)? I mean even now military scientists do their best to outguess and outtech the enemy, surely they won't be different in the future.
Assuming it is not 'magic', but electromagnetic (what else), the shield alone should make it impossible to scan anything - it is a huge electromagnetic interference, as far as any electromagnetic wave is concerned, not to mention the amount of metal armour shielding the ship's hull. Although the whole scan business smells fishy to me.
