why AI declarate war if he is in other side of universe?

Distance isn't part of that one. The penalty is for your fleets sitting inside their borders when you don't have an Open Borders treaty, and it shows up in the relations breakdown as "You have a ship in our territory".

That check doesn't care whether the ship is armed, so freighters running a trade route through their space count the same as a warship would. It also goes on how many of your fleets are in there, not one ship passing by.

Getting Open Borders signed with them clears the penalty.

there should be rly punish for killing civilian ships if they are not in thier terrytory