Many of these problems would be sorted by treating them as ships. I'm sure the only way they will come to fruition in a transport role is if they are SIGNIFICANTLY bigger than even the heavy conventional lifters. Traditionally Airships have been operated by the Navies of the world, and I'd always propose that something of that scale ought be operated by the RN, for obvious reasons, if not tradition.
As with most maritime vessels, a great deal more forward planning would go into the operation of an airship. If the weather was to get particularly bad, It could always bugger orf to happier climes. Big hangars other than for maintenance seem wasteful.
The ballast issue is just trivial. Dirt/Rocks/Other cargo would be your simple answers. How many maritime freighters do you see with no containers on the top? More or less none. In this financially concious age, the RN/RAF airships could drop the troops off, then take on the civilian freight coming the other way- Partially paying for themselves. Logically the efficient way to use these vehicles would be for them to be fully loaded on every leg.
For airships to be of any use in the real world, they would have to carry significantly more cargo than any existing aircraft and be faster than a ship even in bad weather. 100/200 tons of payload is hardly what I would describe as significant, considering that a 'fleet' of 8 C-17's could deliver that kind of package in a day if it was called for. A payload of a few thousand tons however would fill the gap between sea and existing air transport.
When you think that Concorde died and the A380 flew, you see where the benefits of mass transport like this exist.