There are known convertible top issues.
Car problem reports
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Most reported 2001 Honda S2000 problems
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.
A buzzing from the transmission when decelerating from 3,000 to 4,000 RPM can be caused by normal gear backlash noise in the transmission. Honda has an updated clutch disc to help reduce the noise.