It's tough with a young puppy, you don't want to miss it if they really need to go in the middle of the night but as you've learned, they don't always need to go. With my most recent 2, who I remember better than the puppies in the past, their crate was right beside my bed. If they were wire crates, I put a cover or something over most of it, leaving one end uncovered, so the puppy was in a more den-like enclosure. If they started to whimper and I knew they'd been outside pretty recently, I did not let them out, I shushed them, let them sniff my fingers, and they usually would settle down and go back to sleep. The next time they woke up I'd take them out but no playing. If they wouldn't settle and sounded desperate, I took them out- one of them had a round of diarrhea at about 14 weeks of age and her cries to go outside were pretty strident. I'd take them out on a leash, give them some time to pee, which at 2 am always seems to take hours(!) but I probably only gave them 5-10 minutes max, and take them straight back to the crate. Not much talking, cuddling and no playing, just all business. It's kind of a game of roulette, you don't want them to go in the crate but he seems to have shown that he doesn't need to pee every time. Make sure he's gone both pee and poop just before putting him in his crate at 10 pm. I'm not sure these are any "modern" techniques, just the usual.
As for peeing and pooping in his crate, what is his schedule during the day when you're working?