Right, I don't think it makes sense to have our long distance transit vehicle be the same one that needs to decelerate/aerobrake - I'm assuming we'd do something like an Aldrin Cycler for transit between Earth/Mars, where we have taxis that go to/from the cyclers.

In KSR's Mars Trilogy, they had an emergency shelter, seems reasonable if the bulk of the radiation exposure is predictable. But I'd personally feel better being shielded the entire time, given cosmic radiation.