I symbolically linked two drives across a folder located in the program files folder of the C:\ directory. This folder is linked to a much larger/slower HDD. Windows is installed on a small SSD which is the reason for the symbolic links. The problem is that when I install things into the linked folder the available space shown in the computer explorer still decreases. I thought the point of symbolic links were to avoid this issue. any thoughts on why I am having this issue?
The symbolic links are most likely working fine, however when you install an application, only part of it resides in Program Files.
There may be some parts that end up in the c:\windows heiarachy, such as dll files.
There will also be parts that reside in your profile folder - c:\Users\. You'll probably find a signficant amount of space is in your user folder.
One thing you can do is move your entire user folder over to the slower drive, and symlink it back to c:\users. You'll need to log in as a different user to do this.