Well it is a chicks car. You should have seen how many chicks I got with mine!
Anyway I've owned four Miatas; two 1992's, a 1999 standard, and a 1999 10th Anniv. Edition. The latter fell victim to that dreaded #4 thrust bearing problem and had catastrophic engine failure at 3200 miles. Got a brand new engine at no charge, or course. I forget the way to check a Miata to see if it's susceptible for that problem... it involved checking the play in one of the crankshaft bolts but I forget the tolerance. The other thing with that #4 bearing is that, if it hasn't happened by 10,000 or 20,000 miles, it probably won't happen. most failures were almost immediate.
Other things to look out for are the condition of the convertible top. Mine had an issue where the top eventually punctured itself because every time I lowered it, a bolt that wasn't aligned right in the assembly scraped away at the vinyl. The 2nd gens have glass windows so you don't need to worry about the condition of the back window like with 1st gens, but you might want to ensure the defroster works. Other than that, they're pretty much like any other car... check the basics and if they prove ok, you probably have a good Miata in front of you. If the owner has service records, even better. Miatas also benefit GREATLY from alignments... if you want some good specs, look in miata.net for "Lanny's specs".
edit: FORGOT TO ADD... some '99s have issues with a "crunchy" shift from 1st to 2nd, mostly specific to the six-speeds. That is easily resolved by replacing the tranny fluid... Miata trannys rather dislike OEM fluids but get some Redline 75w90 (2.1 quarts) and swap the fluids out and you'll be smooth-shifting all the way down to -20 F. If all 2.1 quarts don't fit... the shift turret (on 6 spds only) will take the rest. It has it's own little cavity for oil, just suck the old out and put the new in. And while you're at it... the shift boots themselves (there's 2) tend to wear out quick so check those too.