IANAL, but my understanding is that the fact that the clone was written from scratch doesn't have any bearing on whether or not it infringes on copyright. The clone uses the name "Agar.io Clone" and copies the look and mechanics of the original game, thus making it substantially similar in appearance and use to the copyrighted work. Unless they have found some way to invoke fair use (educational purposes, etc.), the clone you mention is also infringing.
An analogy: if someone were to write a book called "Harry Potter - Clone" in their own words about the adventures of young wizard, you could expect them to receive a notice of infringement pretty darn fast, regardless of the fact that they didn't copy the original word-for-word.