Flooding the system can only work if the group that floods the system is large enough that it isn't simply expedient for the surveillance organisations to decide you're a potential risk and put you under additional surveillance.
Encryption is in a similar position, but it is a far easier sell to business and the general public, and so the chances of reaching critical mass of communications is much greater.
The interesting bit is that the general public increasing their adoption of better security practices to make them invisible will benefit the pedophiles and terrorist already in hiding because their choice to hide/encrypt will no longer result in them sticking out from the masses.
Most criminals are caught because their groups are targeted and OPSEC (operational security) is really, really hard. They catch the people who didn't maintain strict discipline and get them to flip on the rest. This is an age-old recipe which is resistant to technological change because, again, OPSEC is really, really hard.
I think the idea was to use a DDoS-like farm of hacked machined to constantly send random messages and packets meant to trip their detection systems to random other IPs, thereby increasing the sheer amount of noise surveillance authorities have to deal with and false-positive "suspects" (the owners of all those hacked machines).
Naturally, that still doesn't solve any other problems...
Encryption is in a similar position, but it is a far easier sell to business and the general public, and so the chances of reaching critical mass of communications is much greater.