Ion cannons targeting enemy weapons is essentially a free ride for the first 4 sectors of the game. Yeah, they do no hull damage, but that's what attack drones are for! While your drones pick at the enemy, they are frozen with useless weapons thanks to your continued ion assault.
In the first 4 levels the game is highly unlikely to throw something at you that you cannot simply Ion into nothing... but by sector 5 you better watch out. Enemy shield levels are now powerful enough to completely block your ions (assuming you only have one cannon) so you better have built up the rest of your weapons systems!
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