I was actually once involved in working on a web app, which we eventually almost ended up marketing as a standard "desktop application". For some reason, Marketing got it into their heads that one of our major clients wanted the product to "appear to be a GUI application", so we created a little Windows app that just hosts the IE ActiveX control, and points to our web app (hiding the fact that it's actually a browser). So effectively, to an untrained eye it looked like the product was a standard GUI app.
Granted, this isn't exactly what you're asking (we were still pointing at a web app, and not hosting the whole thing locally) - but it's close enough. It would have been trivial - minus some of the remote web services it used - to set this up to just have the whole thing sitting on the local machine.
Here was the biggest problem though: look and feel. Especially feel.
People expect certain behaviours from rich GUI apps (drag and drop, native-feeling windows and dialogs, etc). It is extremely hard to get a genuinely native look and feel from a web frontend. There is simply a different user flow in what is expected when you open up a web app in a browser (eg. Gmail), as opposed to when you use a rich GUI application (eg. Outlook). In my experience, trying to equate the two is asking for trouble. If you put out a "GUI app" which acts like a web app, you're likely to be flooded with usability and LAF complaints.
TL;DR - Web apps and GUI apps have different looks and feels, and a different user culture to some extent. While it's technically possible to do something like this, from my experience, I wouldn't go there (again). At best you're likely to end up with a horrendous mix of client-side scripting that will be more difficult to learn, use and maintain than doing the whole thing as a normal GUI app in the first place. And people WILL complain about things "not quite feeling right" for a native GUI app. It's tempting to think that they won't - but they will.
I have never actually found a visual designer that makes it easy to create robust designs (if anyone has any they like, feel free to correct me). They are nice for dumping stuff on a fixed-size window to mock things up, but when it comes to making something that resizes nicely, plays well with DPI and themes, and all the other stuff that separates a professional UI from a merely "good-enough" one, they honestly become more work than just coding it up yourself (assuming a decent UI framework to play with).
Visual designers are excellent for rapidly prototyping software, trialling designs, and playing around to see how stuff looks, but I wouldn't use one for the final build.
Best Answer
It is not bad practice to use GUI designer to design your forms, GUI. Esp in Visual Studio. They are there for this purpose and are extensively used.
In web development, it is a different story. It is a bad practice to use GUI designer (for example Microsoft Front Page now superseded by WebMatrix). The reason
So as far as your question, it is not bad practice to use GUI in design forms esp in Visual Studio. Not at all.