I am too experiencing many crashes especially at Mt. Horn. I think it has something to do with the rendering of specific pokémon/sprites – although not sure, I'm playing with randomized pokémon, so crashing often at Mt. Horn like you would be a coincidence I guess. So there is probably more to this.
I tried playing through Mt. Horn with DesmuME and melonDS. Both are crashing pretty regularly here for me. I once got to a floor and was able to reproduce a crash after the game tried to render a parasect. With save states and a lot of trying I could get around it using long distance attacks, so the parasect was defeated before being rendered. However, in another playthrough through Mt. Horn it did *not* crash after encountering a parasect. Very strange. My current approach is to save state before entering a dungeon if necessary and playing all floors until I get through crashless. It's very painful since this is like my 10th attempt. Wish me luck.
Edit 1: I needed 3 more tries to make it all the way to Fogbound Lake. All the crashes happened at Mt. Horn. After that no more.
Edit 2: I progressed further into the game and stumpled upon many freezes. I noticed that some dungeons are fine and some regularly cause freezes. Now I'm at the graduation exam mission at Mystifying Forrest but I can only make it to floor 4, there I got a freeze 5 times in a row now. I really hope that I'm not hard stuck here and try to figure something out if it happens again but atm I don't know what.