So on the nexus, if you swipe to the right you get the google now screen which I really like. However, if you swipe to the right on an HTC it gives you blinkfeed, which I don't like. With 4.4 overwrite this and allow us to have google now as a homescreen?
A launcher is just a shell, or an app that responds to the Home button.
Android 4.4 on the Nexus introduces the Google Experience Launcher or whatever they called it in the end, that was the rumored name anyway. This is the launcher app which includes the Google now pane.
With HTC Sense 5 and 5.5, the launcher is written by HTC and called Prism (leading to one or two funny threads about people worried about this "NSA Prism" thing found on their phone). This application is the one that includes Blinkfeed on the leftmost pane.
So, when HTC updates the One to Android 4.4 and Sense 5.5, what will happen with the new KitKat google now pane?
Nothing.
Blinkfeed will still be there, because it's part of the Prism launcher, while the Google Now pane is part of the Google Launcher.
HOWEVER since the Google Launcher has been confirmed as becoming a part of the Google Search application, it may very well be easy to change your launcher app to the Google launcher instead of using HTC's own launcher, enabling you to get something that's closer to the stock Google experience - losing the ability to use blinkfeed and the HTC widgets in the process, though...
In fact you won't have to wait for 4.4, as APKs are already available that you can download and install on your phone to get the new google search and launcher. These will make their way in the Play Store eventually...