

In Desmume there are random colored screens in Kirby when going in certain doors and Pokemon has the 'black dots' when walking around problem.

Tl dr: Not currently possible in mainline Desmume. Comparing the libretro cores (the MelonDS core was just updated to 0.9, Win64 build here), MelonDS has better graphics emulation of Kirby Super Star Ultra and Pokemon SoulSilver. Old OpenGL had problems with 3D itself, while Softrasterizer had alignment issues with 2D. Leaving it native and aligning it to a CRT (Set to a 384 high resolution) is also an option, if you feel like going through the effort.
DESMUME RETROARCH CORE WINDOWS
OSX version of Desmume also has support for multi-pass post-processing shaders and filters which Windows version currently doesn't have.Whether that is simple Nearest 2x or some pixel art scaling filter like HQx or xBRZ is up to you. Make sure OpenGL and Filter are checked under Display Method. The only other real thing you can do is filter it.Turning it on helps the serrated edges of ultra low-res DS polygons and lines smooth out, appear to wobble less during movement, and retain their shape better when viewed from distance. DeSmuME's OpenGL 3D mode supports Multisampling Anti-Aliasing(MSAA).Method Z seems to work the best in most cases. You can try setting your windows power plan to High Performance, since Balanced can sometimes throttle your CPU in RetroArch. So your newer CPU shouldn't have a problem with even the heaviest settings.

