At the time of replying, they have added (don't know when) a way to remove layers in Adobe Acrobat Pro DC, though the process is annoying at best.
- Select one of theses tools 'PDF Standard', 'Optimize PDF', or 'Print Production'.
- Select 'Preflight'.
- Change the profile at the top of the page to 'Acrobat Pro DC 2015 Profiles'
- Under the 'Layers' tab, click on the 'Remove layer with specified name'.
- (If there are multiple layers you wish to remove, I suggest renaming all layers you wish to remove to the same name)
- Input the name of the layer you wish to remove into the 'Name of layer:' field and click 'OK'.
- Once the process finishes, the layers will be removed (not hidden).
Hopefully this helps those still looking for answers.