It's been a requirement to reveal what is in whuch transport all through 5th under 'Note on Secrecy' (and 4th IIRC) and it's a requirement now. Color-coding units really does nothing any more given that units can embark into someone else's dedicated transport. Makes the shell game easier in fact. I've heard the "I write it down" and the "slip of paper under the transport" etc etc. Doesn't matter. If you're required to tell me, then just tell me.
Don't know if the story about Jervis is true or not, but someone did try to pull the old shell game on me at one of the US GTs (which also addresses that 'trust' issue, just how much are you going to trust someone you've never met before). Guess he forgot that I had videotaped the deployment and each movement phase and was able to prove to him that the destroyed trukk was indeed the Warboss and not just boyz as he claimed. So yeah, it is a potential issue and I for one am glad that such rules exist. If you and your opponent want to play secrecy, fine, go for it. However, don't expect me to agree to it.