Caps aren't necessarily MEANT to take out snubcraft, unless you load then down with anti-snub weaponry like flacks and gats.
That's the whole point of having diversified fleets when you fly around, instead of tanking around in your battlecruiser trying to kill everything you see/want.
As for decreased agility with higher armor - not all armors necessarily mean "heavier" in terms of mass. Some higher grade armors can just use stronger alloys that actually weigh less (think titanium vs iron). So that comparison doesn't necessarily follow
