IMTU Universe the weapons of choice for trade war are EMP missiles that will force the target to stop for repairs and hopefully go into port. In port sabotage is frequent. Normally lives are lost only by accident and a good time is had by all. The normal "rules" are framed accordingly. For instance it is bad manners for a guard to wear armor during a trade war because then an attacker will not be able to attack with a tranq dart and escalation becomes more probable.
Sometimes though it escalates to the point of using deadly weapons. This is regretable.
In either case the war ends when one parties expense reaches a point where it must concede. Or when the State becomes impatient and forces an end. Say because it is starting to escalate to much, or because trade is being disturbed, or the balance of power is being knocked out of kilter.
This refers to a situation where both parties have the same homeworld and are thus well refereed. When this isn't true things are a bit more difficult.
The EMP solves the problem of what happens if the crew refuse to be nice and surrender. That is the most likely outcome but there might be a cultural prejudice against it, or the crew might have their own financial stake in the voyage. But if the ship is temporarily damaged and forced into port it doesn' t matter as much.