I have many things to respond, initially my comments were "not so nice" considering the tone of your post, but instead I'm going to try to educate you as much as possible with the disclaimer that A. I am not a lawyer, but B. I did happen to have my office right next door to one of our IP lawyers at one of the video game publishers I worked at, so I did learn quite a bit about this over the years...
First of all, please do not go telling the homebrew publishers how they should be operating or what they should or shouldn't have on their website. Instead you should be THANKING THEM for keeping a console alive today that hasn't seen a retail shelf in 35 years and arguably should be dead and forgotten about, but thanks to these people and this community, we still have new games coming out for a 1982 console today.
Secondly. a homebrew publisher can make whatever game they feel like it, and publish it however they want to. That includes using original company logos on a box without permission or using an IP without obtaining the rights to it. And sure, they all run the potential risk of having the IP owner send them a legal document telling them they can't do that, and of course they would have to stop doing that, the reality of the situation is this...
There are many companies out there that actually do see the VALUE in "un-official" products because it keeps their brands alive in ways they aren't interested in spending money to promote their company or that brand. And usually the reason why they aren't interested is because whatever platform or situation that un-official product is being released in, probably wouldn't generate them enough revenue to be concerned with.
Example: Let's take Disney for a moment. Just take a second and go search "Minnie Ears" on Etsy. You will find TWO HUNDRED AND FIFTY pages of people selling un-official Disney Minnie ears many of them using actual logos and Disney characters without permission. And it is very rare that Disney has ever gone after any of these Etsy shops for copyright infringement. Why is that? Because while Disney is not profiting off of all these Minnie ears directly, they are absolutely gaining indirectly from them. Social media posts from people wearing them to Disney theme parks. Often times someone who buys un-official ears are also going to go looking for the official ears. Disney doesn't have the capacity to produce the volume of these items that everyone else is doing, and they know that it is an extension of their own brand IN A POSITIVE WAY, so they allow it.
And yes, Disney could go after every single one of those Etsy shops, but the reality is that it would probably cost them more money in lawyer fees than it would generate them money by stopping the production of these un-official products.
Now back to games because a similar situation applies here.
I don't know why Nintendo doesn't allow more "unofficial" homebrew games to be published. Hell, they even cracked down on the Super Mario Bros Commodore 64 port which wasn't even being sold! But the one thing I can say about Nintendo is that they have always been protective of their IP and they have every right to be. I do not believe any one is getting rich from doing homebrew games or reproductions of rom hacks. Last I checked there were not a lot of "millionaires" in this community who also double as homebrew publishers, and trust me, as someone who has worked for some of the biggest game publishers in the world, I know the difference between "making games for a profit" and "making games out of passion." And there is just not enough profit in homebrews for those big name publishers to worry about those unofficial games.
Sure, Konami, Namco, or any of the other publishers could go after homebrew developers if they wanted to. I see plenty of Pac-Man and Castlevania hacks or homebrews being created and sold all the time. But like the lawyer that used to have his office next to me, it would cost the company way more money to have him go after these smaller projects, it would generate much more paperwork and headaches for these these companies, than if they had that same lawyer doing something more productive like negotiating deals with new IP parters for the publisher to develop games on current generation console.
Every single homebrewer, Etsy shop owner, eBay store front, etc, that develops and sells unofficial games runs that same risk. But I feel like in many ways there is an unwritten "handshake" that some publishers have made with the homebrew and hack communities that they have allowed these games to be made and published.
To be fair, Nintendo doesn't go after everyone. There are tons of Zelda and Super Mario hacks out there being sold every day on cartridges complete in box from many reproduction homebrewers out there. And yes, they run the same risk. And while some may disagree, I don't see this being any bigger of an infraction than doing 60 in a 50MPH zone.
And that's just my two cents based on my 22 years of working in the video games business, and another nearly 10 years of being involved in the retro gaming communities.