First, the only way the hyper-loop or any other very high-speed, high-efficiency transportation system can possibly work is in a low-drag environment. The only way to establish low drag is to lower the air pressure. There aren't windows because the vehicle is in a tube that's been depressurized. If they reach the target speed of 700 mph, windows wouldn't help regardless. The terrain would move by so quickly that it would be nauseating and disturbing to most people inside. Even on high-speed trains, like the AVE in Spain, it can be difficult looking out the window for any length of time.
The way you would alleviate discomfort would be to have large displays that could show something interesting, sort of like the elevator that was built for tourists at the One World Trade Center. Or perhaps fit people with VR goggles. It may not work for everyone, but transportation systems can rarely perfectly accommodate the entire population. Many people refuse to fly due to a fear of heights, fear of crashing, discomfort with security screening, etc.
I'd presume they would always know where pods are located within the system. The pods are self-powered and would surely have emergency backup systems. In addition, they'd probably have spare pods that could operate within the tube at a lower speed for the purpose of towing or pushing stranded pods to access points. That might not even be necessary if they space the access points regularly enough. The pods would surely have a very long stopping distance and could be programmed to vary the amount of braking pressure to have it stop at or near an access point. They'd likely have bulkheads every mile or so in order to be able to service the tunnels without needing to pressurize the entire route. Those bulkheads could be used to isolate a section of track and quickly pressurize it.
None of these are insurmountable problems. But they will take time to develop and test without a doubt.