What kind of hardware acceleration are you talking about exactly ? What you need exactly ? There are different kinds.
Yes you can enable the OpenGL open-source driver, and chromium will say that GPU acceleration is active, but from my tests, there are no benefits of running Chromium with the OpenGL open-source driver unless you need WebGL, for the contrary, you will loose video hardware acceleration for example.
If there is a way to use OpenGL on RetroPie, short awnser is no. At least not an easy way, and even if you could make some emulators work, it would be worse using de open-source driver.