Well, from what I know, I'm guessing that the ship didn't have its shields online at the time since the main Space Battle had already taken place and there was no need for the Carrier to have its shields on line at that time. As for its hull strength, I don't know how thick the hull strength of a Carrier is but its thinner than most human ships I think. (Think about Halo Combat Evolved and the campaign level "Keys". You have to jump through a hull breach and from memory the hull there was only 3 meters thick or so.) So my bet is that since High Charity had just exited slip space and was travelling at an alarming speed, the velocity of the pod would have been enough to enter and exit the ship.
But I don't understand how its weapons got disabled though......
That pod could have damaged essential parts of the weapons systems.
From what i know that a a weapon system runs under that area of the hull and that if that area is cut then it disables most if not all ship weapons.