SharePoint Web Services use WCF which runs "side-by-side" with ASP.NET within IIS and thus do not get logged within the HTTP pipeline. 
https://msdn.microsoft.com/en-us/library/aa702682.aspx

I tried setting `<serviceHostingEnvironment aspNetCompatibilityEnabled="true" />` in the web.config, but it didn't seem to help.

I successfully enabled WCF tracing by Following https://msdn.microsoft.com/en-us/library/ms733025.aspx.  I then had great fun Using Service Trace Viewer for Viewing Correlated Traces and Troubleshooting (h ttps://msdn.microsoft.com/en-us/library/aa751795.aspx).  Unfortunately, its too verbose to leave on and is not as easy as IIS web logs.