I work at Nando's.
The company are well aware of the leak to their revenue the loyalty cards can be, however, given the current 'boom' Nando's is having as a company in addition to the fact that the loyalty cards bring in more money from genuine customers than is lost, they just don't care.
They've been trialling E-loyalty cards, similar to what you'd find at Subway or a casino, in Scotland and they will be rolled out sometime this year I think.