Heh, look up "vacuum cannon" on youtube. The tunnel would need to be slowly depressurized, otherwise anything in it would turn into a bullet when the atmosphere rushes in.
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.
You don't need a full vaccum. Even half an atmosphere would greatly reduce air resistance and allow for 4x the velocity in 1 atm.
Humans can survive (uncomfortably) at .5 atm and you eliminate the vacuum cannon problem simply by putting pressurization valves periodically throughout the tube.
Hyperloop is not a full vacuum, only partial vacuum if I'm not mistaken. I don't know what kind of difference that would make on pressure but I assume that means that the tubes are not air tight and actually breathe.
Hyper-loop requires 99.99% of the air to be removed from the tube, so it is complete vacuum from the lethality / safety and structure / pressure perspective.
I am not sure what do you mean by 'ubes are not air tight and actually breathe', but they definitely are not air permeable.