You don't need to kill connections or increase the number allowed. You need to fix a defect in the application on one side of the connection, specifically, the side which does not initiate the close.
See Figure 13 of RFC 793. Your programs are at step 3 of the close sequence. The side which you see in FIN-WAIT-2 is behaving correctly. It has initiated the close and the TCP stack has sent a FIN packet on the network. The side in CLOSE-WAIT has the defect. The TCP stack on that side has received and acknowledged the FIN packet, but the application has failed to notice. How the application is expected to detect that the remote side has closed the connection will depend on your platform. Unfortunately, I am old, and don't know node.js or socket.io.
What happens in C is that the socket appears readable, but a read() returns a zero-length packet. When the application sees this, it is expected to call close(). You will find something equivalent in the docs for node.js or socket.io.
When you find it, considering answering your own question here and accepting the answer.