Michael,

Regarding modeling "extra" systems for conditioned spaces, the key is
"conditioned" spaces. See the definition of "conditioned space" in the
standard. If a space has no heating or cooling, it is not a conditioned
space. The User's Manual for ASHRAE 90.1-2004 clarifies that "This
requirement only applies to conditioned spaces in the building.
Semiheated spaces would only have a heating system; unconditioned spaces
would have neither heating nor cooling systems." (p. G-21) See the
definition for "semiheated space" too. I believe the intent here is to
add a cooling system to spaces that only have a heating system and add a
heating system to spaces that only have a cooling system.

If the model is for LEED, the LEED-NC v2.2 Reference Guide clarifies it.
"For areas of the project without heating or cooling systems (such as
parking garages), there is no need to model heating or cooling systems
in either the Proposed or Baseline Designs." (p. 181)

I don't know of any restrictions on the thermostat settings, so you
might be able to just make the thermostat setting of the fictitious
system pretty extreme so that the system rarely (or never) comes on.
This would satisfy the requirement to have a system, but keep your
energy consumption numbers more realistic.

Sincerely,

Keith Swartz, PE, LEED(r) AP