First of all, let me congratulate you with your desire to report an honest view of your projects. It is a cliche, but in the long run this is the best way to operate. Projects have a tendency to require a deliverable in the end, and you can wiggle what you want during some phases in the project, but if you don't have anything to show for it in the end, there is no way you can talk you out of that. Of course being honest doesn't mean being blunt. There must be 50 ways to bring news, so always stop a short while to think about the best way to put things. I am not saying to make things overly nice, however, "You stink" can also be formulated in a different way.
There is no 100% guarantee that your team members are telling you the truth. It all comes down to a matter of trust. Do you trust the information they provide you? And in return, do your team members trust you? Do they know their heads will not be chopped off when they bring bad news? Do they trust you for not putting them through the Spanish Inquisition if they inform you of something they did wrong? The only reasons people will hold out on bad news is if they fear the consequences. Trust breeds trust. This loop should start with you.
You also can assist your team in making better assessments of the situation. Ask then questions; how and why. Ask scenarios: what if...? Ask for analogies to previous situations. Ask for their assumptions. But make sure they understand you do this not because you question their decisions, but to help them improve them. There is a fine nuance here. Sometimes, discussing a situation in a group setting can also improve the "honesty" level of the information.