You might not want to pop the emergency hatch when you're surrounded by vacuum.
This also applies to any sort of failure that compromises the vacuum. A dipshit with a rifle could kill anybody in the system in a fraction of a second. Burying the tubes is probably the only way to avoid this, but thankfully the whole thing is vaporware anyway.
Humans can survive (uncomfortably) at .5 atm and you eliminate the vacuum cannon problem simply by putting pressurization valves periodically throughout the tube.
I am not sure what do you mean by 'ubes are not air tight and actually breathe', but they definitely are not air permeable.