I've not played either security or antagonist since this testmerge was implemented but observed a lot. It's kind of a mixed bag, really. In itself there's no issue with security having access to fourty-fives, a lot of antagonist gimmicks tend to follow a timeline like this:
- The ship gets boarded, antagonists might be armed but peaceful, introducing their gimmick.
- Antagonists (or Security/Command, more rarely though) escalate the situation in a way they see fit, given antagonists are usually armed head to heels, security usually full-equips through the armory.
I think fourty-fives are more soulful overall, but the "...armory will get used less..." argument isn't really true. There's very few antagonist gimmicks that actually follow a step-by-step escalation, most notable would be revolution here, most other gimmicks tend to go as I outlined.