Someone in a comment a few days ago, who was themselves asked to write such a letter for someone they knew who was charged and ultimately convicted, made an excellent observation:
Defense attorneys are very likely to have requested those character reference letters way before the case even made it to trial. So it's entirely possible that Kutcher and Kunis wrote those letters long ago, based on information they had at the time, probably thinking the charges were unfounded.
Now, obviously, the easy solution to that would be if they were to come out now and tell whether that happened or not, and make clear what they think now. Which is what I would do, but I'm also not a Hollywoo celebrity with publicists and handlers and lawyers.