I gotta say. I really dislike topics like this where people just make a narrative without any attempt to justify it or evidence they really thought about it. So, let's ask a few questions to see if the point the OP is making is valid.

1. How well did remakes/ports typically sell on 3DS?

Ocarina of Time, a remake of an N64 game released early in the 3DS lifespan, sold about 5 million copies. Majora's Mask released a few years later, sold about half that. Donkey Kong Country Returns sold about 2 million. Fire Emblem Echoes sold just under 700k. Hyrule Warriors sold about 500K. Mario and Luigi Superstar Saga about 500K. Poochy and Yoshi's Wooly World, and Mario Party top 100 (more of a compilation) also sold around 500K. Star Fox 3D under 1,000,000.

That's not every single one, but a good sample. There's a lot of variance, and the main factor seems to be sales of the original. DKCR sold between 1/4 and 1/3 of what it did on Wii. Majora's Mask has sold about 2/3 of the N64 version. Ocarina about 2/3. Superstar Saga about 1/4. Hyrule Warriors between 1/3 and 1/4. Yoshi's Wooly World around 1/3.
Star Fox around 1/4.

The Zelda 64 remakes seem to be outliers, but generally, we should expect a remake to sell somewhere in the neighborhood of 1/3 of the original. Unfortunately, not a lot of original Gameboy games have been made, so, we don't have any of those to compare. At any rate, our data shows Metroid 2 at about 1 3/4 million. So far, Metroid Samus Returns sold about 28% of the original. So, a little more than a quarter, and a little less than a third. Which is just what we'd expect, compared to other games.

2. How did games released around that time on the 3DS in general sell?

Yokai watch 2 sold about 3 million. DQ11 1.8. Monster Hunter XX 1.8. DQVIII 1.14. Miitopia 1m. FE Echoes 700K. Wooly World 500K. Yoshi Wooly World 500K and Mario Party about 500K. Ultra Sun and Moon about 6.5 million.

Only 5 games sold over a million. Aside from Pokemon, which is an outlier in terms of sales, those games generally had the bulk of their sales in Japan. Except for Miitopia which for some reason sold really well in EU.

3. How did remakes around that time on the 3DS sell?

Let's put those two things together to find a pattern.

The best comparison would seem to be Mario and Luigi. It's a first party remake of a game that had similar sales for the original releasing around the same time. And the sales are about the same. Mario and Luigi sold very slightly better in absolute numbers, while Samus Returns sold better in relation to its base game.

The next best comparison (and possibly a better one) might be FE Echoes. Echoes is more similar to Samus Returns in the sense that it makes far elaborate of a remake than Mario and Lugi. Echoes and Returns may be better thought of as reimaginations. Echoes sold about 700 K. A bit better than Returns. Which I'd kind of expect based on the trend we see of Japanese sales tending to be better for the 3DS at that time. In fact, Echoes sold about 50K more in the US, and about 150K. So, the difference in the sales of the two games is almost entirely explained by the higher sales in Japan.

Otherwise the sales are really close to Yoshi and Poochy's Wooly World and Mario Party Top 100, which are another port/compilation released at the same time.

In conclusion, your position that the game's sales are "beyond bad" is... well, beyond bad. The sales are in line with other remakes on the 3DS, in line with other titles released at the same time, and most significantly, in line with other remakes released at around that time for that system. The sales are pretty much exactly what should be expected, and I'm guessing are pretty much exactly what Nintendo expected. Unless they had really strange expectations, the project should be profitable for them.