I assume you're using the FPS++ mod. If so, go into BotW's graphics packs > Mods > FPS++ > Fence Method > change the Active Preset from "Performance" (default) to "Fence Skip"

It's worth noting that I'm using Vulkan + async rendering via Nvidia's Vulkan beta drivers instead of OpenGL, so I can't guarantee this will work for your system/setup. But, for me, changing that setting stabilized framerates to a near perfect 60 and reduced stuttering by a significant degree in almost every area. There are still some areas like Death Mountain which drop to around 40fps, but I think this is simply due to the number of particle effects, it's still very playable.

System: Ryzen 1600, 32gb of ram, 1070ti, Cemu installed on an internal Firecuda SSHD (not boot drive)

Botw graphics pack settings: 1080p, 200% shadow resolution, LOD bias -16 (highest), enhanced reflections, native AA, no depth of field, grass swaying Vulkan workaround, FPS++ (32 frames averaged, Fence Skip, NPC stutter fix, 60 fps limit)