Meanwhile if a city needs 3/4 of it’s workforce through the door by 9AM, congestion at each hub still occurs, and rush hours aren’t actually alleviated, only spread around. Hub stations will be the same horrible kind of place train stations, bus stations and airports are, unless a new conceptualization of origin sourcing and destination arrival is brought to the table.
The only new aspect that a hyperloop adds to the equation, to change the game is that, theoretiacally, longer distances can be negotiated, permitting any given urban center to import from greater distances than before, and urban residents can interchange between hubs without 500MPH aviation.
Of course, for those promises to hold true, tubes must be cut, and track laid within them. Every mile of interconnection adds compelling power to the principle of the concept. Individual point-to-point connections are meaningless, if there are not many points connected, and the distances aren’t longer than was previously realistic.
Effectively, hyperloop is the capacity of a point-to-point transit system (e.g., airline) with the infrastructure requirements of a train network, or combining the worst features of both systems. You'd have to bore city-center tunnels for every city you'd want to connect to, as opposed to being able to share those tracks (the fact that you can't share intercity rail with commuter rail is a big reason why maglev generally doesn't make economic sense).
The real benifit is simply speed, it's faster than aircraft and no need for extensive security as you can't hijack trains.
* Not that the term seems to refer to any specific design at this point.
You're right in that vactrains are essentially no different than HSR, and that's basically because vactrains are just ultra-HSR. There is some issue about using maglev propulsion versus regular electric locomotive, but that's mostly about being able to share infrastructure in inner-city portions.
I don't think a reasonable sized bomb is going to do much more than kill people in a single car. So, sure some people would die and it would cause some damage, but not even close to hundreds. Basically, the same risks as someone blowing up a buss, which has no real safty checks.
[1] https://en.wikipedia.org/wiki/1977_Dutch_train_hijacking
Other problems include branches and junctions which normal railways can do with no problem.