In the spotlight settings I added my external drive in the Spotlight blacklist because I don't want my shared drive to be indexed and try to avoid all the extra meta-files.
How can I still search for files in the folders of my external drive?
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Well, if you don't index the drive, then there's nothing for Spotlight to search!
One alternative is something like EasyFind, an app which has to trawl through the disk, checking each file against your search terms every time you do a search. It may have advantages over Spotlight, but it's much slower, because there's no pre-compiled index.
Or you can use the
find command in the Terminal.
But really, your fear of "all the extra meta-files" is largely unfounded. The size of the data is quite small, and well worth it for the utility of instant results.