You're actually closer than you might think.  Color association is something marketing teams take into consideration a lot and gold has positive connotations.  On a side note, the only of those I find iffy on its own (as in not relative to another rendition) is Captain Toad, because it is less gold and more just yellow. 

They were

Never realized that. No big deal but I would prefer the original tho.

Looking at the Ocarina of Time 3D box art change makes me worried, I REALLY hope they don't goldify the Majora's Mask 3D box art

I dont think they will, it already has the ESRB logo on it

What annoyed me was the red MK8 box...

Thats a good question actually,especially with Captain Toad

First off I think the golden stuff looks quite crappy most of the time (kinda like a cheap 50 cent pirate skull toy ring) compared to the original ones.
It seems to me like the idea behind that coloring is "Gold=>treasure=>rare=>buy fast before its gone" and hell this worked on me when I was a child. However nowadays that coloring sheme seems sort cheap to me and I think they should get rid of it or make some REAL limited editions.

I actually like a lot of the gold artworks. The Wind Waker ones are good either way imo, and I think OoT 3D is better not gold, but the rest of them I actually like better. I hope Zelda U has a gold box like MK8 had a red one, lol.

They don´t ruin it, it´s awesome.