Was the engine running while the car was in deep water? If so, and the water killed the engine, then yes, likely major engine damage. If you even turned the engine over with the start button without first checking to make sure the intake isn't full of water, you could've hurt the engine at that point as well.
If the engine is ok, in theory the car could be drivable with some work, but that water will have seeped in everywhere. At the very least you'd be replacing all the carpets/fabric, fixing some electrical issues, dealing with early internal rusting from water getting stuck in places where you can't get it out again easily, etc.
Normally an insurance place will total a flooded car because it's damn near impossible to get them back to their previous level of quality, especially a brand new car. Fight them on it.
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