Why don't you want to crate him at night? If nobody is home during the day and he's in the crate for many hours I understand, but a crate becomes the dog's sanctuary, like a teenager's bedroom.
If someone is home all or most of the day and he's only in the crate a little during the day I would just crate train him for bedtime. If he needs to be in a crate while you're away, which is usually because they're destructive in the house or can get into trouble, will you be able to watch him any better when you're asleep? It's really not cruel or mean, most dogs grow to love the crate and will sleep in it and play in it whether the door is open or not..
I had a beagle for a while when I was younger and she was the most stubborn dog I'd ever seen.. The only other thing I can think of is to teach him the off command and use petting and praise instead of treats for rewards. Either that or ban him from the bedroom all together and put his crate in a very public room in the house. Eventually he'll learn that you don't go into his bedroom, and he doesn't go into yours. I would use a baby gate rather than a door to keep him out though. It might make him feel easier if he can see what's going on inside the room, so that he doesn't feel like he has to be worried something scary is lurking in there.. Also with a baby gate eventually you should be able to remove it all together and he'll still realize that there's a barrier there, be it mental or physical.
Was he used for hunting? I know a hound that was used for hunting but given to a friend of mine because he became sort of shell-shocked and started getting very upset at any loud sudden noises. He would wet the floor every single time and run and hide under the furniture or in a closet. They had to be especially careful to make sure he was not in his crate during a thunderstorm because although he loved his den he needed to be curled up to his people during a storm.
In some cases establishing that you are the pack leader might help, because he'll trust you to protect him from harm and won't need to be on edge watching for danger. Then gradually his reactions to loud noises will fade away as he realizes that if it was something really bad, you would protect him from it anyway.. And since you're not doing anything special, it must not be a big deal..
The "I'm not worried about it, so you shouldn't be either" thing might work too if you are consistent in not really cuddling him and running to pet him and calm him when he gets frightened.. That way you're not trying to calm him down for something that he doesn't need to be frightened of in the first place. I would check with a trainer on that though, because some dogs would take that very well and learn quickly but depending on how terrified he really is he might also take it to mean that you don't care and won't help or defend him from dangers..