I would at haphazard guess that Hypixel Studios would use a language they are familiar with, leading to Java being high on my list. We can rule out CSS, as it is not a scripting language, it is just a file format. Also eliminate PHP, Perl, Python, CoffeeScript, and JavaScript, because as these are interpreted languages, they simply do not have the speed to run the game. (Note: these may still be used for in-game scripting, as this code would not need to execute as fast) As for Lua, it may be compiled, but it is not fast enough either. The four with enough speed to run the game, as good looking as it is, are: C, C#, C++, and Java. Most game developers have dropped C for C++ and its better support for objects, so my guesses are either Java, C# or C++ for the language that the game was written in. While I was analyzing the trailer, I noticed the in-game scripting part has a Script type option, so I am starting to wonder whether you can choose out of a few? Lua works very well with C++, but they may have found other ways to incorporate languages into the game. (The one shown in the trailer looks most similar to JavaScript)
Those are my thoughts, but I was very interested to hear all of yours and look forward to seeing what they actually used!
-CodeVortex