If it's a bearing it's very unlikely it'd be covered, equally it would've been easily diagnosed the first time without all of those revisits. Bearings age and the smallest bit of grit/water can make them click and feel rough. They're also one of the cheapest components for a LBS to change (also probably one of the first things they'd have checked before the fork change).
As both of these faults point towards fork/steerer then it could've been a bad batch the first time (and maybe even the replacement). The other issue could've been the same mechanic who built it overtightening and damaging the steerer both times. Especially if its carbon (less of an issue with alu). There's nothing to say the first fault wasn't a damaged/cracked fork (from shipping) and the fault now is a different crack/fault from overtightening when they changed it. Equally it could just be grit between bearing/steerer/clamp (but I imagine any LBS - even Evans & Halfords, would check these & bearings prior to changing a fork).
Do you have a more local Giant dealer you could possibly take it to? Warranty is done by serial/frame number after all...
Disclaimer: I've not listened to the noise but as a Giant Defy owner I've been through 2 sets of headset bearings, 2 BB's and a number of other 'click/creak elimination troubleshooting' scenarios with it.