Does storing bricks in a connected state lessen their longevity?
After researching the question further via some local AFOL, the answer appears to be "No". The tube/stud system remains robust if stored in a connected state. Connectivity issues arise after the studs/tubes begin to wear down due to excessive usage or the elements become cracked. Simply storing a model intact does not lessen the life of the bricks. However, storing LEGO elements out of direct sunlight is recommended.
I have some standard Red 2 x 4 Bricks that have been stuck together in the same configuration since the early '90s, I just separated one and tested it compared to another Red 2 x 4 Brick from the same era, (and probably the same basic building set), but stored loose, and I could not discern any real difference in clutch power.
This is of course highly subjective and a very small sample size, but for at least this one brick 20+ years of being stuck to another brick has not had any noticeable effect on its clutch power.
I would think that other factors such as temperature, exposure to UV light and frequency of use will have a much larger effect on the clutch power of LEGO than being stored stuck to other LEGO elements.
An interesting and related point is discussed in another LEGO Answers question, 'Are transparent neon Lego bricks made from a different plastic than usual?', in which it is stated that elements made of polycarbonate should not be stock together as polycarbonate in contact with polycarbonate creates a very tight bond. (Transparent elements are usually made of polycarbonate, wheres other elements are usually made of ABS plastic post circa 1963*).
- LEGO Answers question: 'How can I store LEGO bricks as long as possible?'
- Brickset forum question on maintaining clutch power: How do you maintain Clutch on Built Sets?
- Answer to another LEGO Answers question mentioning 'optimal clutch power': 'Why are old LEGO bricks more brittle than new ones?'
*Link shamelessly plagiarised from @Joubarc's answer.
Yes, but not very noticeably or quickly.
Keeping bricks assembled will always create stress on the bricks, and will gradually warp the plastic. However, the rate at which clutch power is affected, and to what degree is unclear, and depends on other conditions.
My most pronounced experience with this was a set (6085) that I purchased which had likely been assembled for 15-20 years. Although the elements were shipped disassembled, I had been informed that the model had stayed together, placed on a shelf, and had been dusted before shipping to me.
Although most elements assembled fine, without any discernible clutch loss, a few connections were slightly loose. Upon closer inspection, the loose connections were those where the "dust marks" lined up perfectly-- IE, those particular elements were assembled in that particular configuration for a long time. Rotating those same elements' connection points resulted in normal clutch power, but using the same orientation was looser.
Granted, there are other concerns which may have affected this particular example, such as humidity, UV exposure, ambient temperature, etc. I expect that fluctuations in these other conditions will likely expedite the degradation of clutch in assembled elements.
Having them connected may actually increase longevity, at least for parts of the brick. This shields out light and air pollution. I have several LEGO bricks that were connected for 30+ years, and the sides exposed to air (and Los Angeles air pollution) were significantly more yellowed than the sides that were connected.