For context as to why my mod Modex has empty folders:
I provided them as an out-of-the-box guideline for users to install custom assets to use. Instead of directing users to manually create the directories themselves (More room for user-error). My plugin is setup to look into these directories specifically for assets, but I mistakenly interpreted these directories missing as an "Error" which prompted OP to reveal the issue. My mod can easily be modified to account for these folders not existing, but I think OP has still has a point when it comes to Vortex not deploying empty folders.