There are two great hazards of prolonged space travel that come to my mind. One is micro meteorites and the other is cosmic rays.
The chance of micrometeorites causing damage will increase immensely because of the amount of time the vehicle is in space and traveling and be a huge chance for mission failure as they are not talking of any built in safeguards that I am aware of. There also will not be advance warning for the small particles as radar will not be useful for small particles and they also do not have satellites in place along the route or at Mars that would allow them to choose a path that has has the less space debris.
So what can they do to protect the astronauts and the spacecraft from objects traveling 30,000 miles an hour or maybe even faster? Not much. These objects are traveling so fast that they can pass though thin objects like nothing.
I think the best they can hope for is to come up with some kind of sealing system that would react with the vacuum of space and make a temp repair until a major fix could be made. This could be some sort of membrane that is part of the hull that is filled with a substance that would harden and seal the hole until a better fix could be made.
I have no idea of what could be used myself but I am sure the scientists know.
Also the electronics systems should be modular and compact and entire systems should be placed in one area so that the chances of it being struck would be lessened and you could also have redundant systems in different locations so you could switch from a damaged system to a good one.
All the sensors and switches and keyboards could still be remotely placed but you would want your main brain to be in a protected area instead of spread out over the entire ship.
Just some thoughts.