According to the comments in the Default/Preferences.sublime-settings
file_exclude_patterns) control visibility of folders/files in the sidebar, but not indexing.
binary_file_patterns contains a list of file patterns to mark as
binary. They are displayed in the side bar but excluded from indexing.
index_exclude_patterns supports folder names and full paths to folders/files to exclude from indexing. Not sure how much of the
fnmatch() syntax like
node_modules/** or something like that is supported.