Will Remote Desktop (RDP) continue to work after using IIS Crypto?

Yes. The default security layer in RDP is set to Negotiate which supports both SSL (TLS 1.0) and the RDP Security Layer. However, if you set the security layer to SSL (TLS 1.0) and disable TLS 1.0 in IIS Crypto you may be unable to connect to RDP if you are using Windows Server 2008. To check your settings, open Remote Desktop Session Host Configuration in Administrative Tools and double click RDP-Tcp under the Connections group. If it is set to SSL (TLS 1.0) and you are running Windows Server 2008 make sure that you have installed TLS 1.1 and 1.2 support.

Network Level Authentication only supports the SSL (TLS 1.0 and above) security layer.