It's just not something that's common with these companies. I don't think it's their job to tell us how many, it's their job to make people try to do anything to get one no matter what the cost. On this front it appears they've succeeded.
And if they completely sell out it's a really good thing for them because they won't overproduce. The people who will pass because they couldn't get a special edition are a relatively small demographic if you looks at 3DS sales as a whole and the duration of the special consoles on the markets and in stores.
I agree. It's very rare that I ever learn about the amount for print-runs of Limited Editions. Only one I concretely knew was Drakengard 3 (5000), but most of the time I get the speech "once it's gone, it's gone, so order now!". As long as it sells they're happy and in many cases it's better not to say the amount, impulse buying is a decent factor. For all we know, maybe Nintendo did print 400,000 or 40,000, or etc. there's not indicator that it's 'extremely' limited
Secondly Majora's Mask is a darling to people, myself included. However, I think we actually overestimate demand. Ocarina of Time sold 7.6 million on the N64, only to go on and do 3.35 million on the 3DS. A Link to the Past sold 4.61 on the SNES, A Link Between Worlds sold 2.51 on the 3DS. Majora's Mask only did 3.36 million on the N64, so hypothetically, let's say it does 1.48 million plus new fans, and without some original fans as well. Additionally, not everyone is going to upgrade their 3DS, some will remain with their OG.
So Nintendo goes ahead, designs the console and it's box, prints/manufactures them, and ships them out while taking up shelf space alongside 2 permanent SKUs, plus the 2DS and remaining OGXL. This is all costing additional money for a limited time and what is possibly a smaller audience than both previous 3DS Zelda releases. To me, I'd rather underproduce than overproduce, guarantee that I get a ROI after selling a certain amount rather than having to discount it in time for the next LE 3DS console.
In a perfect world, everyone who wanted the console would get it. But, in my opinion, what Nintendo is doing is not unfounded nor done with little thought and regard.