TLDR: Should I try to kill enemy agents when possible, but they are no threat during mission (and capturing them is not an option)?
Is there any after-mission advantage in killing enemy agent in mission? Does it matter if enemy agent is identified/exposed?
Only thing that comes to my mind would be battle experience.
To be specific, I am in early stages of game and I know that capturing enemy agents is useless for now, since they are automatically questioned and killed without any gain. In mission I completed all objectives. Unidentified agent was on my way to extraction point. I could either kill him or sneak around him (without any problems). I also had mission where killing enemy agent was secondary objective (probably because he was exposed?), but I am not sure if it brings any advantage and how it differs from case where it is not objective.
There seems to be nothing in official manual and I searched steam discussions but there are mostly questions about capturing agents or other in mission details. I also checked Fandom wiki but Agents page says nothing about enemy agents and there is no "Enemy agents" page.
What I am NOT asking is what advantage I have during mission. I know agents can go investigate, destroy documents when they have any suspicion.