So on the original Gullywash underneath last point (Where the small health pack is) was filled with water though I think Arnold removed this fairly on in development though so very few people probably actually played that version.
Hildreth was right about Infused (Former Twisted Play) creating the term River. IIRC it was because the song Riverside was big at the time and they needed a name for that place of the map so they started calling it Riverside as a bit of a meme and because they were one of the teams who played it the most—as it was only just coming out and wasn't in the regular map pool yet—the term just got adopted by others through pugs and mixes. Obviously, it was shortened to river for convenience.
I'm less sure about cheese on Snakewater but I always believed it was because you would check that area for a 'cheese' play aka a soldier or scout hiding there. So you'd check for any cheese plays while capping mid to ensure your medic would be kept safe and that was the most common area for people to hide when the map was first popularised.
Other than that most call outs are named about something specific in the room or area that made it unique. I'm pretty sure shithouse came about because it was either a shit version of actual house or more likely because it looked like an outhouse aka a shithouse.