It's fiction, and therefore can be constructed to prove anything.
Second-guessing history is an amusing pastime, but no more than that.
You make a good point re: Richard III keeping the princes locked up while public opinion turned against him. If he didn't do it, somebody working for him did ("Will nobody rid me of this troublesome priest?")
There are four or five guys who've been touted as suspects. Given the distance in time, and the lack of information even then, we can never know.
They disappeared. Nobody knows what happened to them.