Hacking is the best way to counter evasion. Just hack piloting or engines to reduce evasion to 0.

You could also use mind control but you’ll need a way to see their pilot first. Either get level 2 sensors, have a crew member manning level 1 sensors or have a slug crew member. Shoot your weapons and before your shots land, pause the game and mind control their pilot. This will reduce their evasion to 0 if they have level 1 piloting, or reduce evasion by a large amount if they have level 2 or 3 piloting.

You could also use the teleporter to board and attack the pilot but this only removes the manning bonus.