From what I understand, Spike doesn't list prepatched games on a certain site that romanticizes CDs, wherein the patch creator explicitly requests not to, via their patch documentation. That said, the connectivity between that site and the patch-only site, while tenuous technically, could indeed be legally connected.
Why'd I have a feeling you ware talking about Spike?
IIRC their other site stores the ROMs elsewhere (like a different server), and at one point you needed random keys to get links. I guess them having both that and this new site could make some a bit flustered, but who else is really doing this type of stuff for sake of retro gaming?
As for the legality stuff...personally I wouldn't mind if every Nintendo, most (not all) SEGA etc. games were removed from these sites, because those publishers still actively publish those games and re-release them semi-periodically in their own packages & services. Basically, those games aren't hard to find legally at all, and are fairly priced.
But there are SOOO many other games which are basically abandonware, that will never likely be published again, never seen again, never get official translations in other languages, and if you can find copies of them they command crazy prices ($200+ for a single game, in some cases reaching thousands). And if it's a rare arcade game that never got a (good) home port? Good luck finding a working machine...that doesn't cost $5,000+....
I think for that stuff, these types of preservation sites are essential and it's a shame certain companies want to take them down wholesale. That's leaving a ton of games lost to the void of time, arguably great stuff that's better than a lot of games coming out today. So a small suggestion to such sites: if you
HAVE to have old Nintendo, SEGA, SIE etc. games hosted (wouldn't recommend for above reasons but hey), store them on isolate servers, separate websites, with keys as links to downloads. If you're gonna host those or other games on the main site, make sure they're most likely abandonware or games that will likely never get translations, official re-releases or new copies at normal prices.
Because in
those cases, I say it's fair game to host those games. Their publisher doesn't care, the publisher may not even exist any longer, and IP rights could be tied up among a crap ton of different companies in who-knows-what fields (this was the case with System Shock for a very long time).