How do high traffic sites service more than 65535 TCP connections?

You misunderstand port numbers: a server listens only on one port and can have large numbers of open sockets from clients connecting to that one port.

On the TCP level the tuple (source ip, source port, destination ip, destination port) must be unique for each simultaneous connection. That means a single client cannot open more than 65535 simultaneous connections to a single server. But a server can (theoretically) serve 65535 simultaneous connections per client.

So in practice the server is only limited by how much CPU power, memory etc. it has to serve requests, not by the number of TCP connections to the server.

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