Some Mangaka research their subject material, in full, some research 'some' of their material, some just make things up blindly (for convenience or otherwise). This seems to be the latter.The convenience of isekai language. Some do a translation skill, some don't even bother with that.
Fat and protein are what vegetarians and especially vegans need to consider the most. Just calories, not so much. There's plenty of staple food you get from the earth. That's always been the main source of calories outside areas where fishing is predominant.
But tomatoes being a bit sour isn't that abnormal? Depends on type and all, but still.
It's kind of weird to have a city so close to the sea, but not actually connecting to it. Especially if it's the only port city, there'd be a bustling cityscape at the docks. What's drawn there isn't a port city, but a city adjecant to some small docks.
The way she's saying it sounds like cleaning the sand is some kind of special concern.
Potations and lingonberries was the typical starvation food here back in the day. You can survive entirely on that for quite some time without any major deficiencies. Potatoes are relatively nutrient rich, and most types of berries have tons of vitamins.
Still, somewhat a surprise given Japan is an island nation, but there ARE inland places away from the ocean, so theoretically it would be possible to have never seen a port. Then again, it's also easy to assume things about the distant past, such as having an entirely walled populated area with the docks outside of it...