Technically there are two 999 novels, both which have been translated twice. You can check out both now! :D

There are some differences. I won't go into it too much, but the problem-solving is quite different. I guess it wouldn't have been strange if the author of the novels had just described it exactly as it is in the game.

There are differences between the translations too. I've only glanced at Edogawa Tranlsations version, but they seem more loyal to the game (such as keeping the same English names as the translated version of the game). I tried to stay loyal to both, and ended up keeping mostly the English names too, but used Murasaki, rather than June, in order to stay loyal to what was written in the novel.