Make shielding and CIWS make it harder to board ships they are mounted on.
For CIWS, make them take shots at boarding parties before they can land on the ship, the boarding party speeds ranked based on how fast their parent ships were moving.
For shielding, make boarding parties deal damage equal to their defensive stat to the shields (this stat is combined if multiple are being launched at once) directly to the shield. If this fails to bring the shield down to less than the Attack power of the boarding parties, make the parties essentially "fight" the shield multiple times simultaneously until either the shield breaks or the boarding parties are killed before entry. The "fight" treats the shield as having Attack, Defense, and Morale equal to it's power. If the party defeats the shield, then it moves on to the insides of the craft.
With these two points in mind, it may be more viable to buff the boarding chance of such craft at low speed, as they're not a simple kill-switch against slow craft that don't have onboard marine-headquarter brigades.