Because it’s associated with Valve.

It's not. It's not on Steam, it's not distributed by Valve in any other way. It's located on GitHub, therefore "associated" with Microsoft in that it uses Microsoft's code hosting service.

Just because someone technically commits a copyright violation and Valve usually shrugs this off, doesn't mean that they're Nintendo's contact.

Also, and most importantly, APIs fall under fair use: https://arstechnica.com/tech-policy/2021/04/how-the-supreme-court-saved-the-software-industry-from-api-copyrights/

Valve not being protective enough of their own IP and letting this stuff slide is not what Nintendo wants.

Nintendo did not ask the game to be taken down, just as Nintendo didn't even initiate the takedown of Dolphin from Steam several months ago. It was Valve who initiated the contact to Nintendo back then. That's why Dolphin is still on Github.

Also I don’t think it’s actually using any Valve made assets right?

WTF, I get lectured by people who did not even bother to watch a playthrough on YouTube? At the very least all audio is ripped straight out of real Portal and then converted. Everyone who even cared to watch only a few seconds of gameplay on YouTube would immediately recognize this.