War and Diplomacy realism: contact visibility

You might be forgetting that from their map perspective, they still knew of your location and chose to persue the war instead of offering truce.

   I'll dive into abstraction to reinforce my position here. Diplomatic contact is abstractly represented in Endless Space, as in 4X games in general. In reality it is handled through abassadors, envoys, back-channels, intelligence, leader to leader meetings, etc. All of this is abstracted away and distilled down the the diplomacy interface. So in theory, some form of that abstracted contact would probably have alerted your empire that yes the Hissho empire still stands in some unknown location and yes they are still in a state of war with you.

   Even if they had accepted a truce with you after you took their core systems, it is reasonable to think that their empire would have wanted to maintain some form of relationship with your empire for purposes of commerce and if relations got warm enough some kind of deal that would allow some of their people to migrate back to their home planet as subjects of your empire [I know this isn't a possible in-game action, I'm speaking from a lore perspective], or more accurately (knowing the Hissho temperment) gain the stability needed to rebuild their war machine and tear their home planet from your unworthy grip by force. I know I'm really exercising my imagination here, but imagination is necessary to cope with the level of abstraction that makes 4X strategy games structurally playable without the need for heavy micromanagment.

   I'm getting away from the main point now, but the reason I look at it like this is because any given war between nations does not last forever. 4X games that allow for war, peace, alliances, betrayal, etc. between empires are much more interesting to me than games that put you at perpetual war with opposing factions, eg. Ai War: Fleet Command. The evolution of diplomacy and politics is deeply nuanced. I mean look at Japan: they went from merciless Bushido to Hello Kitty. They did so while embracing their conquerers as partners in a new social order. War literally changed the face of their nation, as it has done so for many nations. This is why I like ES2, I feel it captures the dynamics of diplomatic and political relationships in a unique way, one that has a hint of authenticity compared to real life on Earth.

tl;dr I see where you're coming from, but I politely reject your suggestion because space opera :)