>>23388265
The term literally means "wooden horse", but it doesn't just mean "a horse that happens to be made out of wood", but rather refers specifically to the children's toy.
Which makes sense, since it was an insulting nickname that the Clover executives gave to the White Base's original design when Sunrise presented it to them.

In any case, the name has nothing to do with the mythology of the Trojan Horse or the ship's role in the story.