It might be worth investigating individual problems before considering a reinstall. My impression of the three problems you listed is that they are problems that are and should be solved without an OS reinstall.
If you really want info on a clean install, feel free to skip to the section after the line (starting with "As to reinstalling,").
Apologies if the following information is not useful to you.
You may want to try reinstalling XCode and figuring out whether you need to import certain Frameworks into your programming projects. Most problems I know of with headers and such are related to the XCode install and not to the OS, since XCode.app from the App Store contains not only the app, but the Mac platform SDKs and such as well (it's slightly clunkier than the previous /Developer location, but solves problems with distribution on the App Store). And note that XCode 4 has dropped MacOSX10.6.sdk, so any projects that depend on it need to be modified to use newer SDKs. I am assuming that you haven't done something odd like remove /System/Library/Frameworks.
If you're talking about trashed and deleted applications still appearing in Launchpad, if you try to launch them it should turn to a question mark if no other app by that name exist, and then Launchpad should offer to delete the entry when you click and hold, even if it's not a App Store app. You can also try refreshing Launchpad's entries. This seems to be a problem for all Mac OS X installs. I put the Applications folder as a Stack in Dock instead as a holdover from pre-Launchpad, and I usually launch specific apps with Spotlight (command+space), and I'm not aware of any issues with trashed applications reappearing in the Applications folder or in Spotlight.
As to reinstalling, this forum post (specifically post number 4) suggests that a reinstall will not touch the Bootcamp partition. Hold Command-R before the Apple logo shows up on boot, or hold option on boot and select the Recovery partition. If that doesn't work, you can look up a way to force the App Store to redownload the Mountain Lion installer and use that.
I have used the Recovery partition to reinstall Lion, and it did not require me to reinstall Windows. But that was a re-upgrade rather than a reformat clean install (I think I was having a problem with the Keyboard & Character Viewer). I haven't done an actual clean install since getting my Mac in 2010, despite using it for development and installing software like Virtualbox and Macports packages. Still, that's only been my experience with it, and it may not match your experience.
As always, back up your data from both partitions, just in case. If something goes wrong, the Recovery partition should be able to restore your Mac partition from a full backup.