OP - do you think it annoys you because you judge it as unnecassary, but fear that actually, it might be that he sees it as necessary, and you see his decision to shower as a sign he must be deep down thinks you should shower in the mornings? (Bit like the people who get really wound up by non-drinkers, as if their choice not to drink must be seen that they view themselves as better than the drinker, even if they've not said anything about it at all.)
Some people do get very very wound up by people making different choices to them, that by the very act of picking to do something different they are telling you that you are wrong. (this does seem to be amplified if the other choice is sometimes viewed as 'better' or 'harder' by society)
Think carefully, if you are doing this, then you need to stop yourself, he is chosing to wash to a level that suits him, (and as others have said, is probably showering for other reasons than just cleanliness like relaxing) it is not a sign he thinks your routine is wrong for you, and make sure you aren't taking umbridge at other people making other different choices to you that in no way effect you.
My parents believe there are 2 ways to do anything in life, their way and the wrong way. They find it very hard to accept people making different choices to them when they have the same options. It's like it offends them, and something as petty as washing habits would get them wound up - my mum has told her own sister off for hoovering a wooden floor in said sister's own home because my mum would have swept it with a brush. I had to hear about it a week later. My mum views the hoover for carpets only and wooden or tiled floors are swept then moped. It was not her way and really really annoyed her because it was not the way she'd do it and so had to be corrected, and by refusing to be corrected, my Aunt clearly was picking a fight with my mum by effectively telling my Mum she wasn't cleaning her floors properly. My Aunt was just cleaning up the dust the way she wanted to.