I have noticed that I rarely develop phlemmy throat-aches in the daytime, but often notice them after I have been sleeping. Is this a recognised phenomenon? Could it be because viruses or bacteria aren't being flushed out by food, water and vibration of the throat from speaking or that one's immune system is lower at night? If it is the latter, why is this?
It's because your mouth and tongue are stationary at night, so you don't move the slowly-drying saliva around to lubricate tissues. The mucous tissues dry out, resulting in greater friction with muscle movements (like swallowing), and your body is slightly dehydrated after 6-10 hours without water. If you've ever undergone surgery where they intubated you (stuck a tube down your throat to ensure air supply), afterwards it's a very similar feeling to waking up with a soar throat because your throat dries up and the anesthesia prevents muscle movements.
Your immune system actually works better at night and requires rest to work efficiently. Bacteria and viruses don't really care about the time of day, although the muscles of the larynx do ensure that the mucous layer is continuously circulated. The continual circulation helps prevent debris and bacteria/virii from establishing themselves, although the magnitude of the effect isn't on the same scale of other tactics taken by your body.
Several factors can affect mucous/phlegm/saliva production - including infections, hydration levels, environmental temperature, smoking habits, diet, environmental humidity, and lots more. If it's a constant trouble, you can try drinking more water during the day, a steam humidifier, or talking to your doctor.