I just don't get this debuff at all. I mean, civilian ships are common enough to be sold everywhere. If it's so common, why would it arouse MORE suspicion?
From a reasonable perspective it also makes no sense: a smuggler, spy, or other clandestine persons disguise themselves as civilians to stay hidden. Why does a peashooting paper-dingy arouse more suspicion than an armor-clad bristling-with-gunboat?
From a gameplay perspective, it means you can't use these ships because it's a giant "HERE I AM, COME KILL ME WHILE I'M TOO WEAK AND VULNERABLE TO USE ANYTHING BETTER.". Civilian ships WANT to get by unnoticed because they're being targeted by pirates.
Eh... the way I see it, "civilian" ships have less efficient scanners, which means A) they're less sensitive, thus the reduction in sensor range, and B) they put out more power to try and offset point A, thus the increase in sensor profile. Add on less stealthy engines, reflective instead of absorbent hull plating (think the difference between radar-reflective steel and radar-absorbent carbon fiber), and you get the ingame penalty.
It's not so much that they're suspicious, it's that they're detectable.
For some civilian ships you can get Skins that cancel out the civilian mod: 'hegemony militarized'. I'm not sure it's available for the Venture, but I know it is for the Buffalo.
"Militarized Hegemony Auxiliary" doesn't "cancel out" or even "offset" the "Civilian-grade Hull" penalty.
In the description, it is implied that during the time of the Domain, the Tarsus is a military supply ship that travels in convoys, making it odd that it wouldn't be built to the same stealthy standards as military ships. It wasn't intended to be used by civilians.
The Tarsus was built tough, not sneaky. A freighter suitable for operations within e.g. a solar storm or an asteroid belt. That it often expected to travel in convoys, rather than singly, would make it more likely to be LESS sneaky - why try and hide the convoy, when you can use it as bait for raiders?