Right now when I use ⌘+O to search for files, the fuzzy matching appears to operate over all files in the current project. Unfortunately, this includes
After you setup the search.exclude and file.exclude mentioned on the previous answers, run the command "Clear Editor History" (Use the Command Palette to do that - CTRL + SHIFT + P).
Only after that the excluded files will not appear on your quick open menu.
Update: You can run the command "Clear Command History" too. I forgot about that.