Play in and around the crate, called 'crate games' so he is more comfortable going in and out. Lure him out of his hidey hole rather than pull him out. If this habit is already ingrained then leave a leash on so you can keep him from burrowing under the desk as you are luring with the treat or better, keep him out of that room when it's close to bedtime. Once out don't pop him into the crate straight away or he won't trust the lure. Take him out for a last potty trip, have him help you lock up the house or something but keep him on lead so he doesn't hide again.
I suspect he slept on the bed where he was before. Since you haven't ever allowed him up keep up the good work. He's getting to middle age and has short hair. Be sure his bed is as cozy as your bed is if you've seen he doesn't destroy fabric. My 9 year old seeks comfort, possibly he is the same way. A rumpled up fleece blankie on top of several inches of foam ought to do it.