It seems you are confusing WebGL effects and Audio Effects (advanced audio).
Those are two different things. Android is perfectly capable of handling WebGL effects, but indeed there might be some compatibility issue depending on the OS version.
When you add a plugin to your project in XDK, you have different categories between "Core plugins" to "Third-party plugins".
If you check the "Featured plugins", there are several audio plugins available that could do the trick. My first guess would be to try the "Native Audio Plugin", which seems to possibly cover advanced audio features.
Nonetheless, it is possible you will have to use another plugin, and so will have to find out which one to use.
Be sure to search our forums as well, it is likely you are not the first person to attempt using advanced audio on mobile.