I'm not entirely sure what you meant here... You can mine the energy areas faster if you put more miners, but in the end its still the same amount of energy gained total. The energy areas lose their color (go transparent) the more energy they lose.
What I meant was I could not tell if you gain more energy from one energy area when you put multiple miners on them or if that is redundant. But your explanation answers this.
The hotkeys you have really make the game mechanic a lot better, you should definitly mention them somewhere, because I think you really need to use them in order to stay alive for at least a couple of waves.
One thing that would be neat, was some sort of highscore table. Or at least a personal score, so that you know how good you did. You could give points for each spacecraft kill or just for the time elapsed. I figure that would be easy to do and would add some sort of overall goal to the game.
Also I would prefer if you could not just build your stuff everywhere from the beginning and instead would have to crawl forwards, having to connect every new element with an allready existing one within a limited range. That would add a exploration feel to it.
I ran into some performance issues towards the end with framerates below 10 (have to admit I went a bit crazy on the relay front). I looked into your source code and saw that you don't use openGL. Is that because it doesn't work as an applet?
Anyways great game, much fun :)