You DO NOT lose points for using the ?
PERIOD!
What causes you to miss the simulations is normally you don't know the command syntax and screw that up. Another problem is you spend too much time in the simulation and rush through the remainder of the test or fail to answer all the questions. Any question not answered is automatically wrong. Last time I took the CCNA exam (scored 1000), I purposely played with the simulations to see if I lost points for issuing extra commands or using ?. My score didn't reflect any of the "playing" with the simulations. (Yes, I entered incorrect commands, even tried to reload the boxes, and finally entered the correct syntax before leaving the simulation.) All that was graded was the correct answer.
HTH.