Are we not trying to cure the symptom rather than the sickness?
The symptom, i.e. the floating containers, should never arrise. They should not be in the sea in the first place. The sickness, i.e. putting to sea with a vessel in an unseaworthy condition, is the root of the problem. The problem arrose essentially in the late 60:s and early 70:s when shipping companies started being run by economists rather than seamen. They probably were able to maximise income but they contributed nothing to good seamanship. What they have achieved has gone against hundreds of years of development and increased safety at sea.
Going back to the period of the Second World War, no one would have considered building ro-ro ships of thousands of tons with only one hold! Big ships used to have to be constructed so that they would remain afloat if two consecutive watertight compartments suffered from total ingress of water. The cariage of deck cargoes was normal practise but seamen accepted that they could be washed overboard. Insurance companies did too so that any cargo carried on deck was carried at shipper's risk.
Now we have huge ro-ro vessels, many of which have been lost as a result of the concept along with many lives (e.g. Estonia, Herald of Free Enterprise). We have also containers stacked skywards on deck. Until these practices are stopped then we will continue to see ferries capsizing and containers lost at sea.
Of course, reversing the trend would cost huge sums and we, the consumer, would end up paying the bill. For my part, I would gladly pay another few cents (or in my case Kronor) for a pair of Vietnamese flip-flops but would people on average?
Of course, the issue of tracking containers is an interesting one too. Here again it is economics that steer. I am sure that it is fully possible today to track a "rogue" container. The technology is there but the willingness to spend the money on it is not. Even if containers were tracked, it would probably not be economical to send a ship out to recover them and their water dammaged contents. I am afraid that containers floating arround at sea will be with us for a long time.
Whilst intended in no way as a slurr on their professionalism, good seamanship and economists are poor bed-fellows.