When a capsule is attached on the Trunk, it seems to be only possible to access the Trunk's items. But you can access the capsule's items by going to the pressure view and clicking the pressurized interior of the capsule. The pressure bar should show the pressure of the capsule. Now the capsule is selected and you can access it's items. To switch back to the Trunk, unselect the craft completely and reselect it again.