Why the "that hits" restriction? You massively reduce the viability of support secondary weapons in the fire link (Ion Cannon, Ion Pulse Missile, Flechette Torpedo, Flechette Cannon) by making them even less likely to hit by reducing their chance to fire in the first place.
Because it's not intended to be a carbon copy of the BTL-A4 upgrade. Instead, this is essentially a risk/reward mechanic. You can still fire missiles and cannons on their own if you want to - OR you can attempt to double up and fire BOTH your primary and secondary weapons in the same turn, but you need to hit with your primary first in order to do so.
If you just want to Ion a target, fine, just fire your Ion Cannon. If you just want to fire your Concussion Missiles, fine, just fire your Concussion Missiles.
But if you want to potentially do shed loads of damage, fire your primary weapon instead... and then, IF it hits, you get to perform a free second attack (again, provided you still have the required target lock/focus token when it comes to missiles).
Notice this also makes the Gunboats much more effective against slower, low agility targets than it does against fast, high agility targets - which is both thematic and helps balance the upgrade.
I disagree that the secondary failing to fire if the primary misses (and given that Fire Link involves firing the weapons simultaneously, retroactively failing to have fired) is thematic. Although to be fair nor is BTL-A4 being able to shoot two targets.
Here's an idea for a firelink that prevents the use of damage cannons.
Linked Fire Array
"After you perform an secondary weapon attack that hits, you may cancel all dice results. After this attack you may perform a primary weapon attack against the same target."
Seems useless? It is with Heavy Laser Cannon and Mangler Cannon unless you miss. However, it doesn't affect Ion Cannon, Flechette Cannon or Ion Pulse Missile at all. Assault Missile sort of works although usually the four dice from the rocket itself will be better than a follow up primary attack.
The issue is that it doesn't work with damage missiles.
(Using the Accuracy Corrector precedent here, in that you must trigger the first step to trigger the second.)
Edited by Blue Five