If it's about cloning someone else's site, it's probably not a good idea. A lot of templates out there have specific licenses (e.g. Creative Commons). Some of them may allow you to produce derivative work, although there may be conditions attached (e.g. commercial or not). The absence of an explicit license doesn't imply it's in the public domain.
(I had initially misunderstood the question and though it was about cloning your website.)
It's quite common in the development process of any software product (not just web-sites) to have a development environment, a test environment and a production environment.
To a degree, these could be considered as clones of one another at various points in time in your development life-cycle.
Taking a clone of your current production web-site to modify locally, and perhaps deploy it on a test environment sounds would be in line with such (good) development practices.
Using a revision control system to track you changes would of course be beneficial, as it would allow you to track which changes you've made between the various versions of your "clones". Depending on your familiarity with such tools, you might want to look into Git or Mercurial, for example.