So, I use Dropbox to sync my vault between two computers. There are some folder’s I only want on one of the computers. Can I use Dropbox’s Selective Sync to exclude that, or will that cause any problems for Obsidian when that folder is missing on one of the computers?
Hm. So, you have a file directory like…
Folder
—Subfolder 1
—Subfolder 2
------Subfolder A
Your Vault targets Folder, and you have that same Vault running on multiple devices, only on some devices you want to hide Subfolder 1?
If that’s accurate, I think it’s a little dangerous. If files in Subfolder A are linking to files in Subfolder 1, when you try to access that link on a device that doesn’t have Subfolder 1, Obsidian will create a new note—and then you’ll have two notes with the same name but different content.
Yes, that’s exactly what I wanted to do – and the obvious risk I saw. 
Yeah. Other than that it would probably be okay. So, if you can avoid accidentally linking something in another subfolder, you’re probably fine.
Note that graphs and Obsidian’s cached data (e.g., filenames for autocomplete) might behave a little weird, too.)
I suggest testing it on something small (and with backups) for a bit before going ahead with your whole vault.