An example of clone that doesn't infringe their copyrights (written from scratch, not derived from the original game): https://github.com/huytd/agar.io-clone
Disclaimer: I'm the agar.io developer
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.
"look and feel" are generally a part of Trademark law, not Copyright law. More specifically, Trademark law deals with concept of "customer confusion".
Copyright deals generally with "expression", and generally does not cover what something looks like. So for example, it's possible to copyright the textual rules of a game, but it's not possible to copyright a particular style of game. Which is why it's generally legal to clone something.
It would not legal to do what the person has been been accused of here, which was to substantially copy the original code.
The reason why Trademark/Copyright generally get mixed up with regards to clones is because:
1.) It's actual copy of the original source code, and thus is a copyright violation
2.) It's a "from scratch" clone of the game elements, but mentions the original work in a way that doesn't make it clear to the consumer that it's not actually the original, which is a Trademark violation
3.) It's a "from scratch" clone of the game elements, and mentions specifically that it takes inspiration from the original, but makes it clear that it's not the original. But the original creator doesn't like it, and they are really mad that "anyone can steal my work", and the original creator bills it as a Copyright/Trademark infringement when it's really not.
Assuming the complaint is correct, this is obviously a case of #1. It's been ruled that a literal translation from one language to another is a "mechanical translation", and is not deserving of it's own copyright.
Obviously this is a very coarse overview of a very complicated framework, but should hopefully provide a little more insight in to what the actual law is.
In the main link Agar.io has a very fair DMCA claim if their JS has been literally copied, even if it has than been subsequently altered. However, if one was to make a game like "Bob's Better Floating Balls that Eat Each Other" from scratch, I don't think Agar.io would have a fair claim. I am guessing that they also have a trademark out on Agar.io.
It used this for the server side: https://github.com/OgarProject/Ogar
I doubt Miniclip is going around throwing DMCA notices to companies cloning Agar.io without good reason.
Miniclip SA is a Portuguese company. Can non-US entities submit DMCA takedown requests?
Have a similar situation, my code was obfuscated and somebody just decide to do a reverse engineering and add some features on top, then they put all of this on github under a nice GNU license...
> The Agario game’s distinctive style and graphics are known to tens of millions of players
Colored circles moving around on a checkered grid  is apparently "distinctive style and graphics".
Not only that, it uses language and structure common to all DMCA takedown requests.
Guilty until proven innocent.