I got 2 Xbox 360 wireless controllers for my PC. I'm considering that the Xbox 360 controller won't connect to the Xbox One S receiver (meaning the 360 controller will be phased out soon and games might use a new XInput API that's incompatible with the 360 controller). Can I still do this?
No, Xbox 360 wireless controllers need a compatible Xbox 360 Wireless Gaming Receiver. They aren't compatible with any Xbox One receivers.
See Set up a wireless controller on a Windows PC on this page: