I have a sailing buddy working for a company that is doing R&D for putting SPOT devices on containers that activate upon submersion. Many obstacles to overcome but they are working on it. The ROI is huge so maybe sometime in the future there will be a solution for this. Seems like a really obvious thing to do.
Some of the containers that fall overboard are probably headed straight for the bottom. Others are going to float relatively close to the surface for a period of time. All of them will likely have some amount of sea water inside by the time someone shows up to recover them. I can't think of very many things, shipped in bulk containers, that can be submerged in sea water and still have significant value afterwards.
Depending on the amount of water inside, it might be pretty difficult to get back on the deck of a ship as well. A standard 20' container holds about 1,360 cubic feet, if water is about 62.43 pounds per cubic foot, that would be nearly 85,000 pounds of water inside if it were completely full of water with no cargo (obviously it would be sitting at the bottom if this were the case). But if it was half full of tennis shoes and half full of water, you would still be looking at picking up 50,000+ pounds. Opening the container before pulling it out of the water would significant reduce the weight, but lose most of the cargo (which is probably worthless at that point anyway).
Last time I looked up used containers, they sold for about $5,000, so maybe there is enough value in just the container to send a salvage crew out if they knew exactly where the containers were floating.