Because Echo is a female figure in Greek Myth.
And Echo is also a clone's name in The Clone Wars. The clones were decidedly male.
But given the way clones are designated and name each other, It's probably just that his code starts with E and they were using the phonetic alphabet.
And let's be fair, Most people think of the sound phenomenon named for echo before they think of her.
Quite sure as I watched the episode just yesterday.
http://starwars.wikia.com/wiki/CT-21-0408
Just numbers in his designation. He was called echo for his tendency to repeat orders.