This post is brought to you by [url=https://en.m.wikipedia.org/wiki/HMS_St_Albans_(F83)]HMS St Albans[/url] which is presently parked out the back of my office.
Naturally, being a Nerd, it got me thinking 'oi! 40k! Where's the planet bound naval/water based stuff?'
We've got land battles aplenty, and of course increasing amounts of air power. More if you count Aeronatics Imperialis, despite its currently defunct nature (I say currently, because you never do know)....but nothing on the high seas.
And this is a shame, because it could prove an interesting take on 40k.
Me, I'd do it as two or three 'proper' ships per side, and numerous smaller boarding craft, which would ultimately be the key to winning. After all, the best way to deal with an opposing craft has been to board her, and take out her crew. Indeed this was preferred during the Napoleonic era, as it was cheaper by far to patch up and re-crew a captured enemy craft than build a whole new one. You even got paid for nicking stuff. They called it Prize Money, and it was shared amongst the capturing crew, making it an even more attractive proposition. You should read up on that, it's really interesting!
Hold on. I've digressed, and quite possibly waffled.
Where was I?
Ah yes. But how would this be portrayed? One thing that immediately springs to mind is that Dark Eldar are already fairly well equipped thanks to lots of cheap skimmer. Tau, Astartes, Necron and other Eldar would very likely have skimmer craft, and everyone else more conventional ships (oh, and Chaos could have skimmers. Would explain where they go when a new force of Astartes rebels. After they've been unceremoniously mugged by larger, better established renegade and traitor forces)
Beyond that, I dunno. So I turn to you BoLS.
Have at it!