On the left I have a joined group of 4 planes with alpha textures (texture shown below top image), on the right I have custom leaf shaped meshes in blender, also all joined together as a single mesh. If I wanted to animate these with shaders later (wind simulation), which would be more performant?
I’m afraid it’s not possible to answer this question. The pure geometry solution could be more performant since you have no texture lookups. However, if the geometry becomes too complex, the other solution might be better.
The performance might also depend on the platform and browser you are testing with.
Eventually you have to try out both approaches and compare them for your particular use case.
If you want to do wind simulation, you’ll be doing some kind of vertex animation. In order to get a good looking result, you’ll need enough vertices in order to be able to make it look like the leaves are bending. Regardless of the approach you choose, you’ll definitely need more vertices than are shown in your screenshot.