You could always argue that regardless of production numbers, none of these games are rare if you have deep pockets.
However I think this a very important topic for 2020. When I joined in 2009, MS1 Japanese was about 1k. Blazing star 400-500 and so forth and so forth. It was 5 years after the end of the system but games were easy to find regardless of production numbers. My number 1 question is where the fuck are the games? When is the last time you saw RBS, RB2, MOTW, LB and LB2 US copies for sale? They might as well be phantom games now that you only hear tall tales about. Hell, Metal Slug 2 Japanese was 300-400 back then and easy to find. Now you're lucky to find a real copy in a sea of conversions and NCI boots for less that $3000 US.
Where did they all go?
I believe Mahesak, if anyone can give an educated answer it would be him. I know MS3 had 500 US copies. MS4 had 500 as well, and a handful with the classic art set. MS5 US might be as rare, or ever rarer than MS1 for a US version. Especially with the classic art set. If you want even more rarity try to find the flyer as well. I believe US MS5 was 200-250 copies.
Metal Slug X might also have a production run of 500 for a US version. I know NGF was making "corrected" orange stripe inserts, but I don't know if they were destroying US copies or Japanese copies. If it was US the number would be below 500 for a real US copy.
It's all speculation but its part of the mythic history of this console and a big part of the magic that's felt for AES collectors.