Since we're just speaking about hypotheticals if you dropped a long range missile that can fire across the board without issues to two damage dice you've pretty much ruined it against anything but the low defense ships. It would be the lowest damage potential of any secondary weapon and nearly a complete non-threat against evasive targets.
If the damage potential is the issue then something would be done to limit the maximum. Perhaps it should attack with four dice but only get to deal a maximum of one damage on a hit although that hit could be a critical.