Because it doesn't use conventional chemistry the presence or absence of chemicals, like ambient oxygen wouldn't change the output (like it might for a fuel air bomb) but their their properties might change it. Air will provide some resistance and fluoresce at high enough temperatures. I am curious how big this effect would be though. Debris leaving a nuclear explosion in space would only stop when it hit something and that I think is the biggest flaw with the Orion motor.
If the motor and fuel can be designed so only particles are emitted and somehow ensure that no bullet size fragments are ejected then it seems likely it could be made safe in a practical sense.
That said they at least all seem like solvable problems given enough time and resources.
Build something like the TransAmerica Pyramid (without the two white flanges) and put the motor(s) where the foundation would be as to make the building fly like a rocket. Put the motors on at one G and you get artificial gravity, a slim profile and damage equally distributed along the bulk of the ship and most collision will happen at extreme glancing angles.
Stop off near a comet and melt large boulders of ice to the hull. If the outer hull is tiered whipple shields there will be plenty strong and will serve as mount points for the ice. Run simple heating element through it and simplify the installation of ice as ablative armor.
Have all of the storage on the ship be on walls, cabinets, netting, shelves, etc... and bolt all the furniture down. Because when you aren't accelerating you will have no gravity.
When you want to stop, turn the ship around (using reaction wheels or attitude jets) and blow your engines at the target at 1 G to slow down for the same amount of time you burned them to accelerate. This will create artificial gravity again in the same direction you were experiencing it before because you changed the direction of thrust the same amount you changed the orientation of the ship.
You have a nuclear explosion clearing crap from in front of your ship as you slow down, not as safe as the ice, but presumably your engine(s) is tough enough to withstand a nuclear blast.
Isn't turning the ship at those speeds nearly impossible? You'd either have to slow the entire ship down first (the whole idea) or burn a ton of fuel to turn it while accelerating at a percentage of light speed, while avoiding debis and the spaceships engines explosions. I believe this is why scientists researching this prefer magnetic sails as a means to slow down. Or maybe an alternative engine scheme that doesn't require doing a 360 turn.
The feathers/fletching on an arrow produce more drag and the the arrowhead is dense and moves the center of mass really far forward. As air passes over it the center of mass is pushed back least and the part with more drag are pulled back more.
In space there is no air so rotating the ship is trivial. Consider comets or planets that are constantly revolving. Also, don't confuse turning with changing velocity and direction or travel.
In my previous example the ship would stay in constant motion even though it is turning a 180 degrees. The actual turn could be done with rockets or reaction wheels and by spending very little force to do it.