The software they sell can be purchased agnostic of the hardware they sell. Just because they have designed the software to work on their hardware doesn't make it ethically wrong to run the software on your own separate hardware. Once you've purchased the software, you've fulfilled your moral obligation to the company needed to utilize that software how you see fit.
I talked about this a little while back - back then it was in the context of Bayonetta 2.
I would say that there's a difference if a game is funded specifically to encourage sales of a given platform. From a first-party perspective, it may actually be reasonable business sense if a game makes a loss in its own right if - in turn - it helps boost sales of the overall ecosystem of the console; it can act as a loss-leader to some extent.
Put it this way: If emulation on PC was a big enough market to actually be competitive. Nintendo may not have had reason to fund Bayo 2 in the first place; if emulation were a big enough market to be competitive, *any* game on a platform that can be emulated - even first-party ones - would have to be budgeted and funded with an overall intent of making a profit entirely in its own right.
(Which shouldn't be read as "Therefore emulation is WRONG!", I'm just trying to highlight how the business decisions and ecosystems involved make it not a simple case of "I'm buying the game, I'm running it how I wish, that affects no-one.". It's not necessarily unreasonable to make the point that perhaps all games *should* be budgeted with the intent of making a profit in their own right, for one thing!)
I've been thinking a lot, the last few years, about the whole nuance of financing and budgeting in the games industry. There's a lot of complexity to it, and I think that lends itself in part to the inherent riskiness of the industry of late.