According to BBC and many other sources, islamic state terrorists use a messaging app called Telegram to encrypt communications for groups of users.
On the surface, Telegram developers seem to support high security standards: they have published the spec and API and funded in November 2014 a handsome 300,000 USD cash prize for cracking Telegram encryption [expired in February 2015, the company promises to issue new hacking contests soon]. Experts disagree however that there are reasons to trust telegram and point out many issues with the security of Telegram.
The biggest collateral of terrorist attacks would however be a ban on secure encryption or privacy apps, this has been proposed in the UK but arguably it would be like destroying the very freedom we are trying to protect. Instead, intelligence services are now returning to some more traditional methods, like spies.
What is however missing is reflection on the deeper causes and sources of terrorism, what motivates people to enroll in militant terrorist organizations, and even more importantly the question of funding.
Crypto Currency vs. Terrorist Funding
Even though privacy and encryption are probably going to survive and hopefully will be yet more widely used, it is in my opinion very unlikely that we will ever have a truly anonymous crypto currency which is widely used and accepted.
This could be highly private and based on ZK proofs like in ZeroCash, or just hide the amounts like in CT/CCT proposals, or protect primarily the users and based on ring signatures like in CryptoNote, see fast comparison of features on Fig. 1 here.
However even here advanced cryptography has some tricks to offer, it could be possible to achieve privacy and zero-knowledge proof of good behavior compliance with regulations and taxes, or/and lack of implication in criminal activity at the same time. This actually remains a big question in applied cryptography research if this is realistic. However again cryptography can potentially help to reconcile privacy and policing of organized crime and terrorism.