SignalR 2.0.3 still depends on Owin.dll version 1.0.0.0 just as it has since SignalR 1.0.0.
The only thing defined in Owin.dll is the IAppBuilder interface which hasn't changed since it was introduced. If you look at the NuGet Gallery you'll see that there has only ever been one version of the Owin package.
SignalR also depends on Microsoft.Owin which provides types that make it easier to write Owin middleware. This package has gone through several iterations, and SignalR 2.0.3 depends on Microsoft.Owin 2.0.1.