Do you mean freighters and any other non-military targets (miners, ecomonic/cultural stations, mission/citizen's ships...)?
I find it's a good idea to add a mechanic of dynamic acceptance to war.
Based on ideology, government, war events, population/citizens mix, invoked casus belli to declare the war and localised and global group effect (majority of citizens/pop in your civ endorses war against X.
On planet A, 2 citizens endorse war, 2 are neutral and 1 reprove it. Due to local and global group effect neutral citizens now endorses war; due to local group effect, isolated citizen doesn't protest (get/give no malus) to avoid a fight with his "planetary" neighbours.
On planet B, 2 citizens endorse war, 1 neutral and 2 reprove it. Due to local and global effect, neutral now endorse war; 2 reproving citizens feeling to be a big minority (40%) localy protest against war (they get a malus or completely cancel their own boni) and special local events may appear)
an example among lots of possibilities:
Drengin point of view
_ Drengin civ, with 100% Drengin citizens, declares war against Terran civ with casus belli "We need more slaves and money" what is fully accepted by all citizens.
They attack a planet and decide to raze it completely turning it into dead planet (war event) what is fully reproved by all Drengin citizens because it's opposed to their goal (they lost ships and/or troops without having won more slaves or money).
Now Drengin citizens will accept less depredations.
Terran point of view
_ Terrans, with 90% Terran and 10% Drengin citizens, are attacked by Drengins. Initial conditions: defensive war against Drengins for "more slave and money", every citizens endorse this defensive war, both Terran and Drengin, because they don't want to lose their goods and don't want to be enslaved.
As a defensive war, citizens accept to defend our planets, stations..., crush ennemy fleets inside or close to our borders but not to invade or attack non-military targets.
After Drengins completely destroy one of our Terran planet (war event), Dregin citizens (among Terran civ) now accept to crush ennemy fleets far outside our borders and to destroy ennemy shipyards to prevent another Terran planet's destruction, while Terran citizens accept and want a more agressive retribution.
Terran forces annihilate a Drengin planet (war event); Drengin citizens (Terran civ) reprove it because they're culturally linked to Drengin civ but due to local and global group effect inside Terran civ, they don't protest; Terran citizens accept and enjoy this Drengin planet's destruction and they'd accept more again. But after 5 ennemy planet's destructions (war events), without any other annihilation of our own planets, many Terran citizens become opposed to this way of fight ("we got our revenge, now let's fight like humans"). Now majority will reprove planet's destruction but still accept to conquer Drengin planets to defeat them.
It would be great to have a mechanism of dynamic acceptance of how a war is led affecting involved citizens/populations in the conflict but also external civs, where a war with unrestrained bloodlust can have an impact on diplomatic relations.
I guess it would be hard to integrate and hard to handle in-game, especially for players like me who destroy every ennemy planets except homeworlds.