In the real world soldiers don't walk around packing heat all the time. And even guards are assigned a specific, limited amount of ammunition. That said, it kind of makes sense for SAoY personnel to always have a pistol at their side considering how crazy, dangerous, and random their main opponent, the Mishhuvurthyar, tend to behave. Plus, like Zack said, it seems to be kind of like carrying a sword in their culture.
Saiga's always used a Type 28 SMG as his preferred sidearm because it's the same size as an NSP and can spew effectively unlimited death really quickly. I think it's nice to have NSPs as part of the uniform because letting bridge bunnies and other ship-based dudes repel boarders is always fun.