faulty water pump?

I have had a toyata yaris from new which is just over 3 years old on its latest service (at the main dealers from which i bought it from) a faulty leaking water pump was found the car has done less than 20000 miles this has been replaced at a cost of £220, about 2 years ago the engine started making a rapid ticking noise on start up which disappears after a few minutes when the engine has warmed slightly, the car was checked over at the time by the dealership who said it was mormal and nothing to worry about, however since the new water pump was fitted this ticking has stopped, I am now inclined to think this may have been a faulty water pump all along and should have been replaced 2 years ago while still on its warrenty, I would appreciate any views on this.