A problem can occur with a vibrating expansion valve in the AC system which causes a whistling noise from the passengers vent. Replacing the expansion valve with an updated valve from Honda should repair this problem.
Car Problem Reports
Honda S2000 AC Expansion Valve May Cause Whistling Sound When AC is Turned On
Honda S2000 Problem
Average Mileage: 97,500 mi (55,000 mi - 140,000 mi)
Visitor, 2006 Honda S2000, 55,000 mi
AC Expansion Valve May Cause Whistling Sound When AC is Turned On