Yes, Finding a cheap deal on an auto would be much easier than converting one. The slush-box Miata has a different trans, additional throttle cable, different pedal box amongst other things. I had a friend go the other way (auto to manual) and needed a donor car to get all the misc parts. Even then it was a major PITA. I've seen some excellent cars on CL only to be disappointed to see it wasn't a stick.
Keep in mind, automatics consisted of about 10% of the NA Miatas sold. Then again there isn't a huge demand for them so you should be able to get a good price. Also, having driven an automatic Miata it is much like driving a convertible Civic. Ho-hum...