This is normal, and, of course, it sucks. I agree that going to crate is always accompanied with kong or chew or at a minimum treats at this age.
The major tip I'd add is that you should aim to NEVER let your puppy get what he wants when he is howling/whining. Otherwise, that's what you've reinforced. If you let him cry for 20 minutes and then let him out, he's learned that howling for 20 mintues works. I wait for substantial quiet before letting puppy out.
This is incredibly hard to handle when you don't know if your young puppy needs to toilet. This also doesn't include a dog with any form of sensitive/upset stomach creating diarrhea or very loose stool.
For this reason, I sleep right next to the crate at this age (though I use cover so puppy isn't staring at me). That way I can hear if the puppy is stirring or up BEFORE they start whining and crying, and I can take them out at that time. They learn that a person will let them out without the crying/howling piece. (They also learn that crying does not work).
Assuming puppy is healthy, I'd focus on getting the toileting dialed in - even if it means playing around with meal times & then setting an alarm for every 3 or 4 hours to take puppy out - so you can just ignore the crying/howling part until it subsides.
At 9 weeks, some puppies can't hold it overnight (some can). Middle of night toileting outings are unceremonious. Take puppy out, toilet, reward, back to crate (+ treat/chew). No play, no attention. It shouldn't take more than a week or two for the puppy to mature to be able to go longer in between.
This sucks. There are sleep deprived nights. The first 72 hours are the worst for everyone. It can take a week or two to get much better. It's still better than having months of barking/crying/howling with confinement or separation.