Hostilities go both ways. If they embargo, then my faction should embargo too, yes? But... I would not want my faction to embargo enemies because I want their money! If the enemy is crazy enough to buy stuff from my faction, I will gladly take their money! If NPCs did not have unlimited resources, they too (in general) should accept my money.
If I gladly let my enemies trade with me (I would because I want their money), then most if not all factions should gladly trade too. I guess NPCs can afford to embargo because they have unlimited resources, but that smacks of cheating if they embargo solely because they are aware they are NPC factions with unlimited resources. They should embargo because of their character, similar to atrocity reactions.
Maybe embargos should be a faction setting. Pirates are angry at everyone, but they gladly trade with anyone (even if they need to smuggle). Tri-Tachyon appears to be a completely amoral faction who cares about money and tech above all else. Maybe uptight factions like Hegemony or the Church would entertain embargos.
P.S. Then again, embargos might exacerbate shortages for NPC vs. NPC interactions (if applied fairly), making it easier for the player to exploit for big money.