Here is the most viable reason I found as to why there is no stun on the troika's second hit:
Today, I was doing a jelly king run. I felt like charging my troika, so I did. I went close to a lumber, and charged-shotted it. However, the lumber was halfway through it's swing animation. As the troika hit, it stunned the lumber. As we all know, stun messes up everything. Stunning an enemy during an attack animation will cause the attack to perform immediately. Both the lumber and I ended up stunned and with less health than before our encounter.
Imagine in FSC: You cornered a zombie, you have a half pip of health, and you second swing the zombie during it's attack animation. You are dead, zombie is laughing.
Another reason could be OPness in lockdown. Stun stands as the most effective status ATM only because more people have freeze/stun resistance.
The stun being bad isn't really on zombies. And zombies are laughable now anyway.
Also the stun on second hit isn't guaranteed so it is not OP in lockdown at all.
Anyways, the bad stun is on lumbers, trojans, and Vanaduke. Those with smash type attack. You usually never notice the bad stun on other mobs so it is not a big deal - it is actually helpful on those.
And finally I do not think this is the reason they didn't add stun on Troika second swing.
I mean look at Triglav, it freezes on second swing which CAN be bad, yet they still made it freeze on second swing.