What would cause normal files to be hidden from the Finder but not the terminal?
On BSD you have a file flag that allows you to hide the file. 

$ chflags hidden path/to/file to hide a file. 

You can see the flag with ls -lO 

$ ls -Ol foo.txt
-rw-r--r-- 1 harry staff - 0 17 Jun 15:57 foo.txt
$ chflags hidden foo.txt
$ ls -Ol foo.txt
-rw-r--r-- 1 harry staff hidden 0 17 Jun 15:57 foo.txt