Does PyCharm use dependencies installed in virtual env when accessing the project through Vagrant?
Not enough information. Pycharm is usually clear where the error lies. I'm assuming you correctly entered the path to the python file in the bin directory? 
Otherwise as long as you have requirements.txt just make another environment through Pycharm and try seeing the difference.
I have setup my Django project with Vagrant and everything works well. When I open it in PyCharm in Windows though, I get many reference errors in the code and also "Package requirements are not satisfied" prompts to install libraries. The problem is, these are already installed in virtual environment (I know because otherwise the project wouldn't work at all). 
Is there any way to let PyCharm know that these dependencies are already installed, and let it know where to find them? 
I have already added the project interpreter in project settings to the one under the /venv directory of my project.