Because a ship moves on top of the waves, cabins higher up end up moving more. Cabins in the lower decks move the least and that's probably why Naofumi and Raphtalia were less affected by the sea sickness. I think it's hilarious that everyone only now realized they are fucking illiterate.
I really hope they develop more of his journey with a sequel. The original series had a more classic japanese story to it and they fucking love cliffhangers so I really need some closure.