My understanding of the current system is that the CR of a fighter squadron represents the number of spare fighters available to that squadron which can be prepared rapidly enough to replace combat losses, rather than a system like ships have where CR represents how well-prepared the ship is for combat. So a zero-CR fighter group, like a zero-CR ship, should still have at least one fighter hull available, but doesn't have the ability to replace any losses sustained during the engagement.
The current explanation for the lack of malfunctions is more or less that any malfunction serious enough to cripple a fighter is probably also sufficient to destroy or permanently disable that fighter - unlike larger warships, fighters aren't going to have a secondary power generator to allow the craft to continue to function even if the main blows, because if the main blows the fighter's going to be gone, anyways.
As for the missiles: I would find it easy to believe that it's much easier to give a fighter a full missile load, especially when it can land on a convenient carrier's flight deck, than it is to prepare an external missile launcher. The CR rules have a bit of a disconnect between what happens to fighters and what happens to ships, it is true, but to continue from earlier - if the CR state represents the number of spare hulls which can be readied for combat within the time represented by a single fight, then this would imply that the fighter group at 0 CR has at least one fighter hull which is combat-ready, or at least sufficiently close to being combat-ready that it could be deployed as such. Since there's only the one fighter or flight (because there are no spares and I can't recall if a 0-CR wing deploys the full 2-6 fighters of the wing or just 1 fighter), it's still not advisable to commit such a group to a serious battle, but there's still at least one fighter which can be made combat-ready in time for the fighting.
