Encryptions(not really a big deal even though it's dynamic), packet structure, every command(packet) id and variables changes randomly on every client build, the security systems which can clearly see if you are modfying any game files or using the original client or not. Darkorbit also have choosen the way to check how the bots to detect them. Which requires the developers to work harder to change their systems fast and make it safer.
I haven't actually decompiled any newer versions since 2013, but what i'm seeing and thinking is above. Sorry if I'm wrong or missing anything.
They probably though it's not worth the effort to make it safe, otherwise they could keep continuning. And seriously, bots ruin any game. That's why darkorbit is dead, if they haven't allowed any bots since the beginning, it could still be popular and active imo. I would respect darkorbir for their effort to make the game legit but nope, too late.