I had an S2000 for 4 years and I never had any problems with my soft top. The current owner daily drives it and leaves it outside and the soft top is still fine. I don't think reliability is an issue. You take care of the top and it will last you a long time.
Security with the soft top is the only issue in my opinion. Soft tops are easier to break into. I read numerous horror stories on the S2000 forums. But much of the blame has to be on the owner. If you leave a $300 Ipod sitting in the seat then it's probably going to get stolen out of any car. It's just easier for the thief and cost more to get repaired with a soft top.
Good luck!
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