Keep in mind I don't run a lot of space combat but I'll give this a try.
ION Damage is dealt.
If the ship has no shields then subtract damage reduction then check vs threshold. The damage is then halved to the hit points. If threshold is beat, then the target is lowered two condition tracks.
50 damage to a ship with damage reduction of 10 with a threshold of 30.
50-10 (DR) = 40 > 30 (TH) divide by 1/2 = 20 damage to HP and down 2 condition tracks.
If the ship has shields then subtract shield rating first, then check vs threshold, then damage reduction . The damage is then halved to the hit points. If threshold is beat, then the target is lowered two condition tracks.
50-20 (SR) = / 30 = 30 (TH) / -10 (DR) = 20 / divide by 1/2 = 10 damage to HP and SR down 5, and down 2 condition tracks.
But even myself would like clarification. Am I even close? When is the damage checked vs threshold?
The biggest advantages of ION weapons with ships is the increased range, and higher chance of lowering the targets threshold.