I know the following aren't in:

Vengeance Grand Cruiser

Jovian Battle Cruiser

Dominion Battle Cruiser

Mercury Battle Cruiser

Endurance Light Cruiser

Siluria Light Cruiser

Havoc Frigate

Also the Dominator and Gothic cruisers aren't in, though I think BFK says those are basically Lunar Hulls with specific components.

Chaos Hulls are in the game, but completely unstatted. I know my rough attempt to approximate Space/Power for one of the Chaos hulls resulted in some power/space requirements that were radically different (usually much less) than Imperial vessels, so I gave up because if I actually stated those my players would go nuts when they found out a Chaos lance has more range and half the power.

Cardinal is also missing, also the IA:X hulls that were non-SM specific like the Charybdis class grand cruiser.

We also have the hulls that are named but not statted from the HH books.

Most new ships are probably pre-orders, but most of them would go to the merchant navies, as they constitute 90% of the operating ships and probably somewhat less of the overall losses.