We've talked about this periodically in the past but I happen to come
across something that may definitively decide the matter.
I was checking SERPs from my Webmaster Tools Query Stats page and saw
the following search string, "php cookie decode".
Going to the SERPs for that search string, I see in the results, which
you should be able to see at http://www.google.com/search?q=php%20cookie%20decode&hl=en
that "php" and "cookie" in the URL of cass-hacks.com/articles/
discussion/js_php_cookies/ was/are highlighted.
Even though "php" and "cookie" are tied together by an underscore and
even though the "cookies" in the URL is a multiple of the singular
"cookie" being searched for, Google did recognize them.
Similarly, in the second indented entry from my site, "decode" in the
URL of cass-hacks.com/articles/discussion/js_url_encode_decode/ is
highlighted as well.
Of course the SERPs listings shows other instances of those search
terms in the listing for pages from my site but that it also
highlights those in particular shows that Google seems to no longer
care about whether a hyphen or an underscore is used.
So, it would seem the question in the subject line of this thread is
no longer an issue! Yay!