Would it be safer if Drones carried transponders?
It is of course a good time to begin considering this, and in truth, it's already a consideration. It's also an assumption by many in the private sector that the FAA will mandate this for commercial drones. Recreational drones will not be allowed to fly at high altitudes any time in the near future, however, as companies that aim to autonomously transport clients with drones are starting to test their aircraft, it will be very necessary. 

The difference between recreational drones and commercial drones is largely their operating space. A recreational drone pilot has no good reason to fly anywhere near 1000 feet, though the technology is becoming more easily available to do so. If you operate under the assumption that the majority of drones are likely to be under 1000 feet, you can somewhat rule them out as factors in commercial operations, for now. Recreational drones are also very small, and they are generally looked at as having similarities to bird strikes - the difference is, there are effective ways to get rid of drones, and not as many effective ways to get rid of birds!

Beyond the fact that commercial transport drones would be flying at higher altitudes, they would also be much larger, and could cause much more damage in an accident. ADS-B will no doubt be a requirement for commercial drones (perhaps of a certain size or above a certain altitude), in the near future. The FAA actually broached this topic with the industry at EAA this past summer.