"Even if the British government is successful with WhatsApp, can they do much against free, open source tools?"
Why would they care about open source tools and niche use of encryption? Of course they don't. They are after mass surveillance and use fear of terrorism to push for it. It's very logical of them.
It's not entirely by accident that the UK current ramp up of legalized government surveillance coincide with Brexit, as the UK doesn't actually have a democratic constitution limiting government surveillance outside of the ECHR treaty they signed as a prerequisite for joining the EU/EEC.