Touch ID doesn't work first thing in the morning?
Probably (maybe? possibly?), your finger looks "dead" first thing in the morning. Touch ID uses both capacitive sensing,  which is activated by the slight electrical charge running through your skin, and radio frequency sensing which does not respond to the dead layer of skin on the outside of your finger -- the part that might be chapped or too dry to be read with much accuracy -- and instead reads only the living tissue underneath. This is why you can't unlock a phone with someone's dead finger.

So, one theory is that your finger, when you're first waking up, isn't in quite the same state as your finger later in the day, on the day when you set up your touch ID.

But, this could all be inaccurate.

How to test?

Idea 1. Try massaging your fingers first thing in the morning before trying to unlock the phone. Maybe getting the blood flowing in your finger will make it look right.  

Idea 2. This one would be very interesting. Next time you wake up and your finger isn't working, unlock your iPhone and then use your finger to set up a new Touch ID. Then, the next day, see if your early morning finger can unlock the phone.

Very curious to hear your results :-)