CocoonJS does support WebGL, but iOS does not support JIT compilation for Javascript, so JS execution speed is slower. On most platforms WebGL is a lot faster since it moves more of the renderer code in to our own highly-optimised Javascript implementation and minimises expensive Javascript-to-native context switches, but since iOS does not compile JS this runs slower and seems to be approximately the same performance (although results for specific games may vary). Also IDK if CocoonJS has bugs that cause artefacts in its WebGL implementation, the best way to check would be to run in a real browser with WebGL support.
In short in real browsers WebGL is very much a good thing, but in CocoonJS which only pretends to be a browser, and iOS apps which don't allow fast Javascript, it can be more hit and miss.