I think in the end for me, zako is used to hype up a later fight when the heroine faces a tougher opponent. The more a heroine wins easily, the more cocky she'll seem (even if she doesn't act that way), which kind of gives fans permission to put her into ryona situations.
I never came at it from that perspective(for zakos), but that is a pretty neat take. Especially if you like seeing the protag tag a beating.
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As for my own views on zakos, there are a few reasons I like them.
First, every organization needs henchmen(not every villain, every org). Someone to do the grunt work. Zakos fill out those ranks, giving the organization numbers and making it seem plausible logistically.
Second, they allow lower stakes fight. While not every major character needs to have super important fights, zakos can be knocked unconcious in decently sized groups, without derailing the plot. Meanwhile, taking out a singular important villain could be an episodes work!
Third, I like women. Big fan.
Fourth, I enjoy combat scenes.
Firth, not a reason why, but I always prefer non-fatal. See point three. But also because zakos are usually very weak, so killing them usually feels wrong. I'm not against it ever, if the scene or story justifies it(via evil or a real threat). But I never liked Space Cobra because the MC seemed to mostly take glee in torturous killing of enemies who could barely scratch him. My favorite zako anime is Aika for this reason, and one more.
Sixth, I prefer more militarized/professional zakos. What I mean by this are zakos who seem coordinated, with organization structures, following commands, etc. I also like some sort of uniform. Agent Aika is great, especially with the bridge crew(which sounds so professional it was like I was watching Macross again!!). And Aika is also good with uniform styles, and providing logistics zakos!
As for fates, I'm usually a "zakos beaten and hero moves on person", but for resolving a scene, having them bound and/or arrested is great. That probably comes from the part of me who likes Spiderman.