My husband is very stubborn about taking showers in the morning (I take one when I get the time to take one, sometimes I have to skip mine if it isn't convenient). My husband likes to take morning showers because he says he gets bed-head (his hair ALWAYS looks way too nice, having slept on it or not-he's very critical), and just getting his hair wet again at the sink doesn't fix it, he wants to take a full shower. Also, he is very much into his "routines". He likes certain things he does during the day to be the same as the day before.
I say it is the smoking and pollen combined. If you can, try to get him to take a shower before bed- although I know I would not be able to convince my husband otherwise.
BTW, this is the worst allergy season, I swear! ...and we live in the same area, so I know you are feeling it worse like I am.
Also, maybe it is just laying in that position for a period of time? Like, my congestion gets worse sometimes when I lay down... Maybe the congestion is making it's way to you more when you are laying down and perhaps makes your cough worse when he gets into bed and is just a coincidence? That would mean everything happens the same way every night, though.
You allergic to cats? Has your husband taken a liking to a neighborhood stray every time he goes out for a smoke? LOL:)