The background fluff of Stealth armor indicates that it includes heat baffles (TM p. 206), and it is based partially off of the old Null Signature system (TO p. 336).
Would heat-seeking missiles (to pg. 369) fired at a unit with stealth armor active treat the unit as been any cooler than it really is for the to-hit modifier (for comparison Null sig is treated as being 18 points cooler)