I've just recently been noticing that my ears' response to low frequencies is much less sensitive in the morning than it is at night. I currently have a tune with a very big, boomy kick in it that sounds insane through the cans when I'm listening at night, to the point where I think I'm going to have to reign that in a bit. So in the morning I'll slap the cans on again and actually think about turning it up because it just doesn't sound powerful enough. I've sometimes noticed that bass parts sound quieter in the morning than they did the night before. This is something I've noticed in my headphones, which have quite good isolation so I don't think it's a case of quieter surroundings at night. Could it be that my ears' low frequency response takes some time to "warm up" after I wake?

I believe it's highly possible, although I've never heard of a situation exactly like yours. Ear fatigue is the most common thing I can relate that to. I'm thinking that maybe in the morning your circulation isn't what it is later in the day...just a guess on my part there.
 
 

I work in the optometry business. Blood sugar plays a big role in your eyesight, and how your visual acuity changes throughout the day. It stands to reason that it would affect other senses too.

Yes, frequency perception does change throughout the day, although from what I've read about it I gather that it's mostly the upper-mids that exhibit this greatest change. I imagine earwax has an effect. And if you really want to get into it, you shouldn't wear hats or sit in high-backed chairs when making frequency-sensitive mix decisions. So many variables, it's hard to pinpoint the source of frequency perception variance.
 
I can't hear anything over 16 KHz anyway, so that's a big chunk of the spectrum I just don't have to worry about.
 

Interesting about the eyes because I've often noticed that when I wake up and look at the wall in front of me through one eye and then the other, each eye sees a slightly different color. I've tried it later in the day and don't see a difference. 
 
Yeah Bit I don't hear anything over 16kHz either. Screw those frequencies!

I think it's possible. When I was married? In the AM, I seemed more sensitive to my ex's "complaining?" *rhymes with itching, and then later in the day, the shrill, high pitched "complaining..." seemed easier to tune out? So I would say it is possible that your body naturally filters some things as the day wears on and on. She monitors this forum so "honey? for old times sake?" (holds up one finger) It's up to the imagination to guess which one it was...

I'm guessing not your thumb..................

Your hearing can change in a matter of seconds depending on how you subject your ears to db and air pressure levels. Do a google on ear fatigue. I learned what little I know from a high school bud that went on to med school and is a practicing ear doctor. Based on what he told me I drastically reduced my levels and TIME spent under headphones! I just turned 62 two weeks ago. I have been suffering from tinnitus going on about 30 to 35 years. I attribute it to standing in front of a Marshall Super Lead 100 watt stack all those years in clubs and on the road.
I have set guidelines now in my studio work producing that I never track and mix on the same day. Mixing at high levels never lasts more than a couple of hours at most. Headphones may be used for tracking, never mastering. If it still isn't right, I try again the next day. No deadline is worth your hearing!
I, too, have lived in apartments where you had no choice but headphones. Just try to be very judicious volume and time wise underneath those things. I don't know what your age is but I can tell you, I sure would have taken better care of my hearing back then. I am paying for it now.

Absolutely.... I don't listen to any music in my ear buds until I'm up for at least an hour or so. Radio is different....anything with speakers is fine as long as it's not critical listening.....I tend to review songs on the forums in the mornings..... what does that tell you?
 
but yes, I notice the same thing.... a noticeable lack of bass response on the buds or cans. So being aware of that, I don't do final mixing in the very early mornings. I let the day roll on a few hours and then mix.

Yes there can be changes hormonal balances through the day, the week, the month, the years.
And tension of the day, night, morning, noon, evening, late hours.