Can κυνήγι μαγισσών be used metaphorically?
It's very much used metaphorically. Having been borrowed from English and incorporated into the Greek language, the phrase is used very similarly in both languages.
Or is μακαρθανισμός outdated?
I don't think Μακαρθισμός is outdated but much like the term McCarthyism, for the most part it is used to denote the witch hunts launched by McCarthy back in the fifties, or to describe similar types of witch hunts in more recent American history.
There's probably more that can be added to the discussion, but I'll leave it to someone else.