The default behavior of Version 6 is to not scan nested directories for assemblies. This behavior can re-enable using the Assembly Scanning API.
The API has been changed to an "Exclude a list" approach. See Assemblies to scan for more information.
endpointConfiguration.AssemblyScanner().ExcludeAssemblies( "BadAssembly1.dll", "BadAssembly2.dll");
var excludesBuilder = AllAssemblies.Matching("NServiceBus") .And("MyCompany.") .Except("BadAssembly1.dll") .And("BadAssembly2.dll"); busConfiguration.AssembliesToScan(excludesBuilder);