I absolutely think Desmond was lying to manipulate Charlie into going down into the hatch. He had plenty of time to think about, since he waited a long time to tell Charlie about the flash. He told Charlie the one thing that he knew would make him sacrifice himself (that doing so would get Claire rescued). As for why he offered to take his place, perhaps it was because Charlie didn't respond when he asked him how long he could really hold his breath, since he wasn't sure at that point if Charlie would make it. But for whatever reason, he did want Charlie to go down into that hatch, and he knew it wasn't flooded.