Cannons are a very popular part of the game that get hosed by Munitions failure. Ever had your Outrider get hit by a Munitions failure? Might as well be 3 direct hits.
What does happen in that situation? Is the ship unable to make any attack for the rest of the game? I'm surprised they haven't FAQed that to say that you can discard the title.
The Outrider title only stops primary attacks while you have a cannon equipped. Cannon gets discarded, your primary works again.
As for the problem of adding things to break new upgrades, such as incapacitating crew, diluting the danger of critical hits - it doesn't need to at all. Just add an appropriate number of general effect cards and keep the ratio the same.
I think they can do better than this, even. The current ratio of meaningful vs. useless critical hits is one of the big problems with the current deck. Ideally (IMHO), any critical hit should have some effect on any ship they land on. This isn't all that hard to do. One easy way would be to have combo effects. "Discard your Elite Pilot Talent upgrades to turn this card face down. -4 Pilot Skill." If you've got an EPT, you lose it. If not, -4 PS. "Treat all white maneuvers as if they were red. Action: Discard one crew to turn this card face down."
Please don't get wrapped around the specific examples, they're off the cuff... but I think they'd be on the right track. Target a specific upgrade, but have a fallback effect if that upgrade isn't present. Have an ongoing negative which can be removed by discarding a particular upgrade type. Combo them with stats that every ship has. Suddenly, every crit is a big deal to every ship.
The fallback idea is great, but I would also like to see more crits that can be repaired. It adds more flavour to the functioning of large ships, where they resist long enough to repair some of the damage. For instance Damage Engine and Stunned Pilot are some of the crits that do monumental damage to some ships and yet can never be repaired.