@OP,
Like most any intervention you choose in life, there will be positive and negative effects.
The negative is that I believe that a MBA will keep more heat trapped. Above certain thresholds, the fans should assist in venting heat away. The effect will be negative if the fans cannot dissipate the increased amount of retained heat or if the MBA will chronically spend a significantly higher percentage of its time at higher temperatures but lower than what is required to trigger the fans (causing chronic, subacute damage).
The positive is that your computer will have some degree of greater protection against scratches with the use of a skin or Speck case. I believe the Speck case will offer better protection than the skin from cosmetic damage as well as even from some bumps.
A lot of us obsess about our MBAs and making everything ideal, which causes us to think in more relative terms (i.e. would the skins make the temperature worse). We should, however, probably also think in absolute terms (i.e. what damage is actually done by the skin and NOT is it worse than without a skin).
I don't think in an absolute sense my Speck cases have produced machines that are at high risk of failure, mainly because my fans don't seem to run often with or without the case on my MBA. The temperatures are seem to be reasonable using software to interrogate the temperature sensors.
My MBP 17", however, runs fairly warm in general. The Speck case by incrementally increasing temperatures, may cause greater incremental damage/risk but I still don't think the machine is at high risk of component failure. I monitor temperatures more closely, however, on the MBP.
Of course, I have absolutely ZERO data to support the above. So, use the skin/case at your own risk.