Yes, you should use a shock boot!|
A body down - piston up shock can benefit from a boot by keeping all the dirt and grit off the piston. Importance? What is sandpaper, after all, but a whole bunch of fine grit that chews away at whatever it rubs against. The grit on the piston shaft, over time, has the same effect on the seals inside of the shock.
The shock boot of a body up - piston down shock serves the same purpose as mentioned above. However, a much more important role for the shock boot in this configuration is to protect that piston from dings or nicks from kicked up trail debris. Those little sharp edges will easily cut the inner seals when the piston cycles. Blake of All Pro Auto & Off Road, West Haven, Utah tells us that the number one reason they see for piston down shock failure can traced back to an unprotected piston with some slight piston nick resulting in a damaged seal and loss of pressurization.
Yes, you should leave the shock boots off!
Of course, at this point there are those that would say we are full of s*##% and that boots should not be used because they trap water and dirt inside thus exacerbating every problem we just pointed out - and those people would be correct... when using boots incorrectly, as most do.
The mistake people make is that shock boots are NOT an install and forget part. Perhaps the shock manufacturers fail to say it (or maybe they do but we have never bothered to read the instructions included with shock boots, have you?), but yes it's true. Shock boots need maintenance. Surprised? Occasionally, the shock boot zip-tie should be snipped and the shock boot flushed of dirt, dust and to allow any moisture out. Blake suggests slipping a garden hose in the top of the boot with the water at moderate pressure each time vehicle motor oil is changed. However, moisture is the enemy of steel so the boots will need to be left unattached overnight to dry out.