Fair enough, good point. I suppose if Nintendo is able to make money by spending less money on smaller games for 3DS, that's not a big deal.Except they did release Captain Toad on the Switch the same date as the 3DS.
It's also worth pointing out that developing for the Switch first doesn't magically keep the budget the same; HD asset development takes time and, therefore, money. Samus Returns was obviously used to judge if the Metroid market still exists; a lower budget is favorable for such a game. Likewise, Luigi's Mansion probably wouldn't be being remade at all right now if they had to do it in HD.
You can't just ignore that most of the 3DS games Nintendo is still publishing are low-budget games, many of which are using existing engines (FE, BiS, and Luigi's Mansion all had capable engines before development began). That likely played a large part in getting the projects greenlit to begin with.
But it doesn't change that so many of these games are desired on Switch too, and in the long-run would likely sell better there. A lot of people like to flex the "install base" argument, but as others have already pointed out, how many of those 3DS are sitting somewhere with a layer of dust on them? Not just because they've been supplanted by Switch owners, but because people just don't play 3DS anymore because it's pretty dated. I wouldn't even be surprised if more people were playing GBA than 3DS at the moment because it's aged better and it's retro goodness.
As much as Nintendo might be making easy money there right now, it's only a matter of time before those sales dry up in favour of Switch sales, especially as Switch sales rise. As soon as Pokemon fans migrate over for instance, that'll be a huge well dried up I think. It'd be good for them to do a smooth transition and start putting games on both I think. Not to mention, while you're right in that these games cost less, they'd make even more money by putting them on both platforms, and it wouldn't cost a lot to downport them to 3DS after HD development for Switch either (at least I imagine).