Found it. Understood it. Fixed it. :)
It looks like a bug left behind by Nuget during updates.
In full build log you can see entries like:
Dependency "Microsoft.Data.Edm, Version=5.6.4.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35". (TaskId:13)
Resolved file path is "C:\Program Files (x86)\Microsoft WCF Data Services\5.6.4\bin\.NETFramework\Microsoft.Data.Edm.dll". (TaskId:13)
As you can see, MSBuild ignores installed nuget packages and goes right into PATH's.
After quick investigation I found that it first occurs in Nop.Web.Framework (same happens in Nop.Web and Nop.Admin).
Long story short, edit those three .csproj's and add Microsoft.Data.Edm, Microsoft.Data.OData, Microsoft.Data.Services.Client (and more if needed) references to nuget packages, you can find them in Nop.Services.csproj, or just copy those:
<Reference Include="Microsoft.Data.Edm, Version=5.7.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
<HintPath>..\..\packages\Microsoft.Data.Edm.5.7.0\lib\net40\Microsoft.Data.Edm.dll</HintPath>
<Private>True</Private>
</Reference>
<Reference Include="Microsoft.Data.OData, Version=5.7.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
<HintPath>..\..\packages\Microsoft.Data.OData.5.7.0\lib\net40\Microsoft.Data.OData.dll</HintPath>
<Private>True</Private>
</Reference>
<Reference Include="Microsoft.Data.Services.Client, Version=5.7.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
<HintPath>..\..\packages\Microsoft.Data.Services.Client.5.7.0\lib\net40\Microsoft.Data.Services.Client.dll</HintPath>
<Private>True</Private>
</Reference>
I guess it should be fixed properly by cleaning and reinstalling nuget references, but this fix is enough to keep it running.