I don't see any place in the already congested city centre where a Hyperloop station could be established. There is already very expensive, deep tunnel being constructed only for commuter trains because of congestion in surface traffic between north and south.
The only place for a Hyperloop terminus would therefore have to be outside the city, with added travel time to and from the Hyperloop. And then how would that be better than the plane or the ferry?
I don't know much about Stockholm (though I visited it half a dozen times), but at least for Helsinki there is plenty of room for a Hyperloop terminus in Vantaa, near the airport. And the airport is now connected to the center with a fast local train that takes less than 30 min from downtown Helsinki. A Hyperloop terminus could easily be built near Aviapolis which is even closer to the center than the airport. If you want even closer to the center, you could do what the Japanese have done with several of their airports - build an artificial island. There is plenty of room for one in the Helsinki archipelago. It would not be big enough for an airport runway, but for a hyperloop, yes. I assume that the same is true of the Stockholm archipelago.
I'm not saying that, in final analysis, you're wrong, just that you may not be as right as you imagine.