Has Omega ever been hacked into before?
In the span of his short life in the story? No, the little guy has only been online for a couple months at this point. Though I'm sure Donnie went through EXTENSIVE testing to make sure that he could not be easily hacked by either the Krang or the last of the human settlements. It's likely he did simulations with Stockboy in the early stages of Omega's creation to be sure.
Aside from Donnie himself, there was only one other person who might have had the skill to hack into Omega, but they're long gone now.
















