SuperDuper is not does not sync but...
 

What if I had a two boot drives that were identical except that on the primary drive I have an alias file pointing to a file called Photos on the secondary drive. If I then create a script to backup all files on the primary drive to the secondary drive except Photos and do a Smart Update, will that action delete or change the Photos file on the secondary drive?

If you have a SYMLINK (NOT an alias) that is stored in the exact location as the folder it points to, and you use Smart Update, it won't touch the destination files. It MUST be in the same location. In other words:

Disk 1:

/Users/machster/Photos -> /Volumes/TheBackupVolume/Users/machster/Photos

Disk 2:
/Users/machster/Photos (actual folder)

If you copy disk 1 to disk 2 with Smart Update, Photos will be left alone, and will not be replaced with the symlink.

You must make sure you understand this before you try it. Please, experiment with noncritical data until you are sure you know how it works...

I am not quite clear about the difference between a Symlink and an alias in this case. If, for example, I create an alias of a folder located on the secondary drive and move the alias to the mirror directory on the primary drive, would you consider that a Symlink?

No: an alias will not work. It must be a symlink, which is created using Terminal -- the "ln" command. (Do "man ln" for info...)