I don't see this proposal going all the way, to be honest, it seems too idealistic. I expect it will be perverted into its opposite, e.g. justification for "review methods" that states could apply to "check if your encryption is secure", which would result in compromising that very security. Remember that EU law is adapted at individual state level; for generic stuff like this, there is plenty of space for interpretation by national legislators.
As a supporter of the EU concept, I think this is dangerous territory for the Union, at a time when its popularity is pretty low. I hope I'll be proven wrong.
You are mistaken about Czech turnout though. It's the second lowest of all members: http://www.europarl.europa.eu/elections2014-results/en/turno...
[Edit] For comparison: Turnout in the 2014 US mid-term elections was 36%. In the most recent presidential elections it was 55%.
I suggest you read up on your EU constitutional law. The Commission is nominated by governments (and confirmed by MEPs); the Council is directly composed by national heads of state.
Commission and Council (i.e. national governments, all together) introduce legislation, which is then amended or rejected by the European Parliament (the body built with that election you mention). The first move is always from governments. In 99% of cases, when there is bad EU law, it's because governments wanted it.