How can I filter out unwanted search results in Alfred (ie node_modules folder, caches)

You have a few options since you're on Lion. The Find feature of Finder by default will search whatever folder you're in. The option next to it is called "This Mac" which should look through the computer. You can also go to "All My Files" in the sidebar and then click on the images section header and that should look for all the image files as well.

I looked at some of the saved search files in Finder's application bundle, and for example /System/Library/CoreServices/Finder.app/Contents/Resources/MyLibraries/myDocuments.cannedSearch/search.savedSearch used a format like this for excluding directories:

<key>FXScopeArrayOfPaths</key>
<array>
  <string>~/</string>
  <string>-Library</string>
  <string>-Music/iTunes</string>
  <string>-Documents/Steam Content</string>
  <string>~/Library/Mobile Documents/</string>
  <string>-com~apple~Keynote</string>
  <string>-com~apple~Pages</string>
  <string>-com~apple~Numbers</string>
</array>

So you can exclude subfolders by adding strings that start with a minus character after a full path. Something like -~/Library doesn't seem to work.

You can edit savedSearch files by dropping them on a text editor. RawQueryDict:SearchScopes and FXScope:FXScopeArrayOfPaths seem to list the same paths by default, but just editing the second one appeared to exclude folders at least in Finder.