If there is truly no hardware acceleration available it falls back to the SwiftShader CPU implementation instead of just disabling those features. But if you are using desktop experience in a VM regularly you should probably turn on VirGL or whatever other 3D paravirt acceleration offered by your hypervisor.
As for the title question: I’d say turn it off, it has security benefits too!
This is unlikely unless the majority of the websites you visit are using WebGL or WebGPU.
On that note it actually brings up a good distinction: you can turn off hardware accelerated rendering separately from the WebGL/WebGPU features, and the latter is what should be done for fingerprinting & security benefits via the Disable3DAPIs flag.