I use Wine and Linux and my smoke is black. Proton is a fork from Wine. You are using the Vulkan graphics driver whereas I'm still using good 'ol OpenGL because my laptop is so old. So I'd guess it's a bug related to how Vulkan works, or possibly how Proton calls it. You could try looking posting the bug on the silent hunter 3 page at
www.wineHQ.org but the game has no maintainer I'm afraid. Also try playing with the particle settings in the game menu, you never know... i think Ctrl-P turns the particles off?
I run Linux from an unwillingness to spend money on new hardware just because of Microsoft's marketing department. My problem is that I'm now getting very regular crashes since the introduction of the pipewire audio system in Fedora Linux. There's a bunch of pipewire updates and it all gets better, then Wine updates and it gets worse again. Very frustrating. The root of the problem is my laptop is now 13 years old, so nothing is tested for it and bugs creep in. Which I guess is why the non-evil parts of Microsoft go along with their marketing people...