I think the drums to be a game mechanic.
But it's not.
Muse staff can correct me on this one if it's horribly inaccurate, but I don't believe that it's said anywhere to listen to the audio cue to know when enemies are near, it's just something that happens because of the way the audio cue was programmed and people have noticed.
How aren't they part of the game mechanics? Drums DO indicate enemy proximity. People know that and use that knowledge to their favor.
One can argue whether muse knew what they did there, but as playing special music when enemies are nearby is a rather straight forward implementation I believe they haven been well aware of the effect it has on the gameplay.
Personally, I think the drums have a positive effect on the gameflow. They allow pilots to fly relatively careless, and hence faster, while searching for a new engagements. That's a good thing, as it helps to get players into action quicker.