I can confirm it’s indeed a bug in the search API. Our engineers are working to resolve it, hopefully by the end of the week – it’s a bug in the way a few layers of our system are interacting.
As for the Streaming API, I can not reproduce this bug there – a steady stream of non-zero retweet and favorite counts are to be found there. Newly created tweets have their expected zero retweet and favorites (since they were just created). Newly created retweets have non-zero retweet_count and favorite_count values as children of the “retweeted_status” node, as is appropriate/typical depending on the states of the original tweet and the availability of the data in real-time at the time of streaming (in other words, those numbers aren’t exact 100% of the time due to the distributed nature of Twitter and the deliver-first philosophy of tweets).