Sort of, but not really. Version numbers for .NET are a little confusing since you have the version numbers of the libraries themselves (.NET), then the underlying runtime (CLR) that those libraries use. The CLR is what applications are actually targeted at.
.NET 2.0, 3.5, and 3.5.1 all use CLR version 2.0.
.NET 4.0, 4.5, and 4.5.1 all use CLR version 4.0.
An app made for a CLR will run on any of the .NET versions that use that CLR. So for example, you can run a .NET 2.0 app in .NET 3.5.1, but you cannot run it in .NET 4.0. Likewise, you can run a .NET 4.0 app in .NET 4.5, but not 3.5.
Thus, even in Windows 8.1, you need .NET 3.5.1, so you can run apps that were targeted at older versions of .NET. That's why it shows up in your Windows Update, and will probably continue to for several versions of Windows, since there's still a lot of software out there targeting the CLR 2.0 series of .NET.