i would also guess that the water ships are tougher; barsaivian airships are generally very light, and made of wood. you might get a decently tough theran ship, but then you won't exactly be welcome flying around in one of those

as to greater utility, it has been noted that the serpent river is a truly remarkable geographic feature that make it incredibly appealing to trade ships, and it is worth considering that cities are generally built along rivers in the first place, so the water ships probably do just fine in terms of being able to reach desirable destinations.
perhaps the water ships only require an engine, and the t'skrang can just salvage it if the ship is destroyed, with the ship itself being an otherwise normal hull? that would mean that if a ship is sunk, the engine could be salvaged and the financial loss would be much smaller...
also, it is quite frankly probably safer. if an airship is damaged enough to crash, well, some adepts have a parachute equivalent, but most people are gonna die. meanwhile, if a ship is sinking, especially given most crew are t'skrang, yeah it sucks, but it isn't likely to inherently mean they die (they might be killed by whatever sunk the ship, of course). and i would suspect nasty weather is more of a concern for airships too.
alternately, it could simply be crew. i presume you need (or at least very strongly desire) good air sailors (or sky raiders) to operate an airship, and neither discipline seems to be extremely common except for sky raiders amongst the mountain trolls... and for some reason i imagine not too many merchants are looking to hire on to an air raider ship :p