The trouble with blowing a hole in the tube somewhere to re-pressurise is that whatever is inside the hole is hit by a wall of air travelling somewhere around the speed of sound. There are a LOT of problems with hyperloop not limited to someone walking up to the tube and shooting it with a .50 Desert Eagle, earthquakes, and the expansion and contraction of the tube as the sun rises and sets.

It's definitely the most unlikely of Elon Musk's plans.

The hyperlink won't be a vacuum. It's just a low air pressure chamber. The plan has never been to maintain a vacuum since that's too difficult at such large scales.

Hyperloop is planned to run at roughly 0.1% of sea level air pressure. For the purposes of a discussion about human survival in the event of pressurization failure, that's effectively a vacuum.