Don,
I did the upgrade from 5 spd to a NEW OEM 6 spd myself a few years back.
I had a 5 spd J spec (factory short gears) that I sold. It had come w/ an engine I bought that was imported from Japan...but I had no interest in it.
As far as the 6 spd, It certainly is nice to have the 6th gear. As others have mentioned, the gears are similar to having the "short gears" with addition to the tall 6th. But as you have figured, it can be somewhat expensive and depending on what you can get it for, including the flywheel and single disk clutch/ pressure plate etc and a means to lock out reverse while the car is moving forward. This question comes up often, as to how much or how, or is it worth it... I got mine (new 6 spd, flywheel, pressure plate, disk, and throwout bearing) at "fire sale" prices.. I bought the plug and play Comptech reverse lockout (but at a extreme discount), and did the work myself. Not to hard. Then I sold my 5 speed for (well it doesn't matter how much) and I ended up being into the upgrade for $700. Now obviously that is a hard one to ditto... but I have helped several others on this message board get fair prices on their 6spd upgrades too. These days their are more options for input shaft/ clutch choices. Those choices might help keep the price of the upgrade down too.
I liked w/ my OEM 5 spd having the 3rd gear hit 118 (approx) mph on the limiter... If you are going to stay NA the shorter gears make some sense(SP?). If you plan to go w/ forced induction.. you'll probably have the power to pull the taller (5 spd OEM gearbox) gears w/ no problem. And like others mentioned... maybe their are better places to invest your $$ on your NSX for performance.
Arround town, you'll probably not use the 6th gear much. On the freeway... might be a differnt story.. (especially w/ fuel @ $3 + a gallon). Any NEW gearbox will feel nice and tight, which is nice. But the OEM 5 spd is a good unit too.
I like my 6 speed, but I don't think I might make the choice to do it if I hadn't gotten such a great deal.
There are TONS of opinions here... Hopefully some of them might help you make a choice you'll be happy with.
Good Luck