I'm leaving the solution here as a note in case others experience this problem. I had to look back to this commit: https://github.com/christophhart/HISE/commit/c948b81f7a86f24a8fce4ea81051c73b7129e2b5
There's a folder named JUCE in the downloaded "Hise-develop" branch. You need to copy all the files from the submodule into this folder.
From now on, the Projucer application will be launched inside this JUCE folder.