first, is there anything wrong with your engine when you drove it? you should get the code pulled for the check engine light to find the problem.
there is no way that they can tell if your cylinder wall is scored unless they have a boroscope and very VERY good eyes. this is, of course, if they have not removed the engine heads, which i would see no reason for unless there was something seriously wrong with your engine. any engine scoring would be very, very minute if you haven't noticed the engine running terribly. even very slight engine scoring will cause an engine to run very badly, leaking gasoline into your oil, loss of compression,etc.
check your engine compression first to make sure that the dealer isn't pulling your leg about needing a new engine. also a leakdown wouldn't be a bad idea.
if you DO need a new engine, you can have SOS refreshen your engine to very promising capabilities (stroked or non-stroked), or you can purchase a used one from the forum. i know there are a few floating around the nsxprime marketplace for less than the prices you were quoted...
here is a link to Science of Speed (SOS)'s website where they list their options for turnkey engine replacements.
look at stage 4 and stage 5...both cheaper than what you were quoted a the dealer, and the 3.3L, 3.6L, and 3.8L makes serious power...
they also have engine refreshing programs that return the engine to stock like performance for cheaper than the listed options.
if you want to read up more on the larger displacement stroked engines, you can read threads by member 'ponyboy' and member 'serialNSXer', for their 3.6L and 3.8L builds.
science of speed N/A engine refurbishing
i would first check in with other members around your area and the mechanics/shops they trust to work on their nsx's. this would rule out any misdiagnosing problems and spending money on things that do not need to be fixed...
