How does the fact that some Just-Dice players have decided to use bots to place bets on their behalf have anything to do with the site being a scam?

It doesn't even fit your own definition.  There's nothing fraudulent or deceptive going on.  Lots of players openly discuss their bot strategies, and share their code between themselves.  Just-Dice doesn't endorse the use of bets, but doesn't have a problem with it either.  If your bot breaks and causes you to bet differently than you thought it would, you're responsible.

Again, I'm not sure what evidence you feel would help.  If you want a list of deposits and withdrawals for each user, that's not going to happen.  The same as it doesn't at any other gambling site.