Is it safe to use launchers? I am new to android OS.I recently purchased nexus 5 and came to know about several launchers.They are just mind blowing experience.But one of my friends suggested me not to use launchers as they override native os or something like that.

My question is that is it really safe to use launchers? I don't want to make any harm to phone OS or anything.

Does it clear all data and clean up everything when I uninstall it?

Kindly provide me knowledge of launchers and what are the disadvantages of using it.

Thanks
As with any app:  look at the permissions it requests and think about whether the app legitimately needs those permissions.  There's nothing inherently unsafe about using a custom launcher, but if it requests permissions that shouldn't be needed just to display a home screen, it may have hidden malicious functionality.  (Or it may use them for legitimate purposes:  for example, some popular launchers request permission to "directly call phone numbers" so that they can provide the ability to put direct-dial icons on your home screen.)

To see the permissions of an app you've already installed, go to Settings -> Apps, find the app, and scroll down to the bottom of its info page.  You can also see an app's permissions in the Play store before you install it:  scroll down to the bottom of the app's page in the Play store and tap on "Permission details".

Note that a launcher app will (naturally) know which other apps you launch with it.  That's generally not a problem, but if the launcher app has Internet permission, it could potentially send information about which apps you use to a third party, which would be a privacy violation.

When you uninstall an app, any data stored with the app itself is removed; this generally includes things like customization settings.  But if the app has "modify USB storage" permission, it may have also created files in your phone's shared storage area — the files you see when you plug the phone into your computer with a USB cable.  Those aren't deleted when you uninstall an app, but you can delete them yourself, either with a USB connection or a file-manager app on the phone itself.

A custom launcher doesn't "override the native OS" in any unsafe way.  It's really just a normal app that happens to respond to the phone's Home button.