Would you approve if this were your daughter in the room with a non related boy 3 yrs older?
This is about law, not personal opinion, but I'll answer your question.
Legally there is no problem with the 3-year old and 6-year old stepsiblings sharing a room UNLESS, of course, the 6-year old has some sort of abuse/assault record or propensities.
If you don't like the arrangement go back to Court, present your argument and request the Court to enter a new Order.
And would I approve? Yes, and I'll explain - I would not have a child with a person who had such poor judgment that he/she would put his/her (and my) child in a dangerous situation. Therefore, unless your "ex" has some sort of history of being abusive or neglectful I would feel she continued to act in the best interest of your daughter under the circumstances.
I do believe there's a possibility that the Court will agree with you and up your child support payments so that your "ex" could afford a separate bedroom for your child, leaving custody unchanged.
This part I don't understand - "Could I take her to court to get custody if she fights me on this?" Where are you intending to "fight her on this"? She is totally within her legal rights. Court is the only option.
The other part of this if you are questioning your child and putting questions and answers in HER mind it could very well backfire on you. I trust you are not, but people question children all the time about inappropriate behavior, the Court-appointed Attorney (or Social Worker) for the child realizes it ... and your chances of visitation could fly out the window.
So - go to Court and request a change. There is no law (unless, of course, your "ex" is in public housing) but perhaps you can make a good legal argument.