So it turns out my guaranteed 60FPS comes from 640x480, windowed. Which has made playing this game ... interesting. That itty bitty window can help me see total patterns better, which really helps me milk the shit out of the PoC, but I get in some pretty tight spaces.
I wanted to talk about it using PM but I'm not allowed to do it yet (I don't have necessary amount of posts for now).
Like you, I'm using Linux Mint, NVidia GPU and have performance issues with DDC (average FPS is 58 and something like 30-40 in some parts of stage 2).
I did a quick check of previous games and noticed one thing. While there is no problems with 6-9 games, I have slightly less than 60 FPS in 10-14 games. Well, I know that my PC isn't new but the interesting thing is next. I started to play TH games quite recently. I did my 1CC Normal of SA at this New Year and still have a replay. I checked it now and noticed that FPS isn't constant 60, it always changes between 56-60. But the game shows that I recorded it at constant FPS 60 (and there are noticeable slows: I have some landmarks using music in 4 and 5 stages and now those moments in BGM are shifted a little).
So, my guess that there were some changes in Wine within half a year that made touhou games starting from TH10 play slower (there is a little chance that it related to NVidia drivers somehow but I doubt), I even checked it on clean wine prefix. Linux, unlike Windows, is more difficult to be polluted with applications so I don't thing that these slowdown are here because I installed something strange since that to slow my system (well, maybe I need to check it on clean OS but I prefer not to do it).
So... well, I'm not fond of current situation.