Changing out your shocks will not fix the noise. I have Tacoma 5100's and I've had the same problem since installing the superflex rear springs a year ago. I've heard it called coil slap and apparently it's not uncommon when using progressive coil springs - especially when they include a large stack of "dead" coils.
I have not found much mention of it in these forums, I suppose thats because it doesn't happen for everyone. My thought on this is that many of us carry different amounts of weight in back and if you are heavy enough then they won't decompress except over very big bumps/dips, also maybe if you are light enough (no spare and no hitch) they will stay uncompressed enough that slap will be minimal. I have the stock spare, a hitch, and usually an empty trunk. With that setup I have about 1mm between the coils at normal ride height... probably perfect conditions for slap to occur.
You're right about it being harmless and also about the solution. I noticed it the first time I took it around the block after the install. For me It's not very audible with the windows up but with them down it's very easy to hear. I am very "in tune" with my vehicles and noises bother me. I plan to purchase and install a coil spring sleeve and according to my measurement this one would work:
Eibach Coil Spring Sleeves CS5002, but at $30 plus shipping for a couple pieces of rubber my frugal side has won out so far.