My impression was that Klan's shot didn't do as much damage due to being slightly off-angle since she was in a hurry to get her shot off.
As for the sniper gunpod... isn't speed pretty much constant in a frictionless environment? If the shots are travelling at Mach 3, they'll remain at mach 3, or so I understand things.
That said if Mikhail's gunpod is determined to be more powerful than Klan's cannon, it blows holes into Tak's theory of Zent weapons being better; my interpretation of that scene was that Klan was wanting to assuage her wounded pride at getting saved by Alto the noob. "Sure, the noob saved me, but he did it with a zent gun, and zent guns are just that better!"
