You can delete ~/.gnupg or anything that's under your user's directory. However, it will be created again whenever you run GnuPG or any program that runs GnuPG under the hood, like the APT package manager.
However, you should not delete anything that belongs to root unless you know what you're doing explicitly. If I were you, I'd leave it alone since it'll hardly do any damage to the system.
So, in short -
All user accounts will have a .gnupg directory if they run anything that uses GPG. Since both root and sudoers can do this, it's very common for systems to have multiple copies of this directory.