I think in the 40k world ships might always be a much more niche weapon than they are on Earth simply because many planets wouldn't have significant amounts of surface liquid for them to fight on.
The reality is that the only way you could have 40k ships would be to have them in their own game, 40k battlefields aren't big enough to have combined land & sea battles (although it might have worked in Epic as special rules?), and when they decided to make a 40k based game about ships, they (quite rightly) concluded SPACEships were much cooler than the floaty sort and made Battlefleet Gothic.
I certainly don't think arguments about ships being obsolete in 40k hold any water (see what I did there?). 40k is crammed full of weapons that would be hopelessly obsolete in a space faring military already. If Thunderhawks / Drop Pods / Teleporters were so ubiquitous they rendered naval transports obsolete, surely the same would go for ground based APCs like Rhinos and Chimeras? Main Battle Tanks have been rendered obsolete by helicopter gunships and attack drones in the 21st century, yet they are a mainstay of the 41st millennium's military and don't even get me started on guys who run up bash people with chainsaws when they have perfectly serviceable guns available or horse riders...
Why are these things in 40k? Well do you want to tell the 40k player base that you're taking their tanks away for no other reason than that they're silly?
You're right that Eldar, Tau and Necrons could simply use the same vehicles the use on land so having 'ships' would make no sense, but anti grav technology is rare in the Imperium and getting rarer (no more 30k Imperial Jetbikes in 40k, well okay, one...) so I could totally see them making use of surface ships, and a big gothic style battleship would look awesome, as would cobbled together Ork gun barges and 'Nid sea monsters.