How exclude a specific folder from spotlight search but not from search window?
From my experience excluding a folder from Spotlight indexing will exclude the files/folders from showing up when you do a search in Spotlight (command+space) but will still allow you to open that folder in finder and use the search bar in the top right of finder to search within that folder only. I imagine that the search of an un-indexed folder means the OSX will search in real time, or temporarily index the folder to allow you to do a folder search that has been excluded from the main Spotlight index and then erase it when you close the Finder window.

Just make sure once you've typed in your search word(s) in the search bar that you click the name of your folder/drive in the "Search" criteria in the grey bar that appears (as shown below).



To exclude a folder from appearing in the Spotlight search, and therefore from being indexed go to: System Preferences > Spotlight > Privacy tab, then click the + and select the folder you want to exclude: