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Mostly I see this happen to websites that use what Yahoo would call excessive linking. Unfortunately, it can mean internal linking, external link - linking out to other listed sites in the case of directories or vendor type websites.
Check first to make sure there are not spidering issues with pages or issues with headers and redirection.
We track our visitors and referrals using some code that I wrote and, recently, we too noticed that Yahoo traffic had dropped off to basically zero. I did a search for our site in the Yahoo SERPs and found 2000+ pages in there. I then traced what happened when someone clicked on a Yahoo SERP and found that Yahoo passes so much other text along with the search string that it was blowing my table update and that gave the impression that we were not getting any hits.I trimmed out the excess bloated referral string and the hits re-appeared magically. (i.e. My fault.)