You all basically have the right of it, but just to say it explicitly:
If a crime goes unwitnessed and unreported, you're not going to held accountable for it in terms of criminality or reputation. If a crime is witnessed, but also still unreported, you won't face any criminal penalties for it, but your reputation with whomever witnessed the crime is likely to change and that social cost can have repercussions ranging from that one character not liking you as much, up to that character deciding others need to be told how bad you are and damaging your reputation in the area.
But if a crime is reported and a contract is given to someone to investigate, they can gather evidence of your crime by examining the scene of the crime using the right abilities. If a preponderance of evidence points to you, they can use that to get a bounty token or engage in some kingdom-specific justice process to see that justice is done.
So, more to your point, as long as you don't report the crime and no one else sees it, you'd be fine. If you're worried though, let me assuage those fears: You can also set up your home so your thief alt is allowed to be there, and then no crime would be committed anyway.
Hope that helps! :)