[manjana]

"How do you track their whereabouts and communication channels if everything is encrypted?"

You need to consider what is also unecrypted which may be used.

Given you have a username you can rather easily check whether that username is registered on any other socialmedia-platform; a site like knowem.com lets you search for a username across +500 socialmedia sites.

From there on you can start to interpolate information from usercontent as well as usercontent-metadata.

I think you are the OP, so I will add this also: The security agency properly have software toolsets which are used for hacking.. If you ain't familiar with Vault7 you should definitely give it some reading: https://en.wikipedia.org/wiki/Vault_7

Related to Vault7 there was also a lot of fuzz about 0-day threats which the NSA had stockpiled, these 0-day's may be used for other things not related to cyber-warfare, like e.g. monitoring potential terrorist activites..

Besides this you have whole pentesting-suites like Kali Linux and similars, which may be used to exploit weaknesses on target-machines.