symbolic link vs. alias
Aliases store two pieces of information about the destination file - both the location and a file identifier. Symbolic links only store the other location. For that reason, if you move a file, Aliases are superior since they can often still point at the correct file when a change happens.

Dropbox or moving the files to another filesystem is where things get really messy - what works on one filesystem will often break in another.



As to your overall file organization and filtering / search problem, that's going to be much trickier thing to answer - you'll need something like 20 questions and back and forth discovery with one or more people. There will be no correct answer either since what would work for 4 years of curriculum might fold like a house of cards if you have 25 years of files. Similarly - designing something for 3 TB of digital media would be overkill for someone that worked in thin file formats like markdown text and simple file references to still images and short clips of animation.

Think about a couple things when you look at why your current workflow is failing you:


Can you use spotlight search effectively. For advanced skills, think spending 3 or 4 hours in 30 minute classes over a couple weeks with people that know search, smart folders, tagging, advanced search to find files by date range, EXIF data in images, by size or format. Maybe you have a fine folder structure and could beef up search so you don't need to move files - just put them where they live and find then quickly / used filtered views to locate things you'll need ad hoc during class or lesson prep.
Do you have a good backup strategy. If you do - just delete things you don't need so you don't need to be a search wizard. When you need something - restore it and go (or put it in the cloud so you can restore or browse the archives for an occasional "miss" on what you need in your working set of files. Box.com / Dropbox / iCloud / Google drive complicate this immensely as sync isn't really backup and backup certainly isn't sync. The more you optimize for [search/sync/backup/organization], the more the other aspects suffer in my experience.
Are you working around key applications that miss features. Many applications can handle files stored in other places and plain text is so small you could carry around plain text of the entire Project Gutenberg library of 56,000 ebooks in 900 MB. It downloads in about 45 seconds for me so your situation might need a different way to index and organize based on what your requirements for files and apps are truly. (TeX is notoriously messy in spewing files all over the place - and I did my thesis in LaTeX - I would be hard pressed to use that now for a body of work that needed to be synced / grow / link over years. Perhaps Apple Notes and other apps fill in for things that can't live in plan text / markdown / pdf.)


Please don't take any of these comments as criticism of your effort and plans. I would expect you've thought deeply about how you work and would have changed if it made sense, but it's going to be hard to have an answer here that's broadly applicable to everyone that reads your post other than outlining some of the relevant items to consider and weigh how those items affect anyones current or ideal or optimized workflow.