While that‘s true right now, a big patch called „Economy 2.0“ is expected to drop this week (more on that here and here).
I really hope this will be a successful first step of making the game actually better than its predecessor. Unfortunately the economy simulation is only one of many issues which make me want to play something else after a few minutes of gameplay. I think it‘ll be at least another year until they‘re able to fix all these minor annoyances, which sum up to one very big annoyance. Like not being able to place stuff sometimes without any obvious reason. Or those ugly, steep pathways on lots, when the connecting street isn‘t completely flat. Or missing animations for firemen, which currently only have to drive up to a burning building in order to stop a fire.
Cities Skylines was a better Sim City (2013) and was justifiably loved for that. For now, Cities Skylines 2 is unfortunately just a worse Cities Skylines.
There‘s a great video on that topic by Matt Parker (Standupmaths) which I‘d wholeheartedly recommend.
TLDW: No, terrain elevation isn‘t generally taken into account when calculating a country‘s surface area, though the actual method differs slightly from country to country. Switzerland would be around 7% bigger, if its mountains were to be taken into account.