Kentico 11 can only target up to .NET 4.7 so in an attempt to fully support your .NET 4.7.1 libraries I believe it is copying in those additional facade DLLs. This is based on the .NET 4.7.1 release announcement, specifically this section:
BCL – .NET Standard 2.0 Support
.NET Framework 4.7.1 has built-in support for .NET Standard 2.0. .NET Framework 4.7.1 adds about 200 missing APIs that were part of .NET Standard 2.0 but not actually implemented by .NET Framework 4.6.1, 4.6.2 or 4.7. You can refer to details on .NET Standard on .NET Standard Microsoft docs.
Applications that target .NET Framework 4.6.1 through 4.7 must deploy additional .NET Standard 2.0 support files in order to consume .NET Standard 2.0 libraries. This situation occurred because the .NET Standard 2.0 spec was finalized after .NET Framework 4.6.1 was released. .NET Framework 4.7.1 is the first .NET Framework release after .NET Standard 2.0, enabling us to provide comprehensive .NET Standard 2.0 support.
Reference that led me to this conclusion: https://github.com/Particular/NServiceBus/issues/5047#issuecomment-339096350
I was unable to reproduce your issue in Visual Studio 2017 Version 15.6.2.
I installed a Kentico 11 website project targeting .NET 4.7. I then created a library project that targeted .NET 4.7.1. I added some dummy code to the project to make use of Sysetem.IO.Compression and System.Net.Http namespaces. I added a reference to the project from Kentico and ran a build. No facade DLLs where copied to the bin folder.
This post indicates the issue was fixed in Visual Studio version 15.6 https://github.com/dotnet/sdk/issues/1647#issuecomment-364999962