I don't think the HDDs will spin-down in a Fusion Drive, as that could potentially add huge delays when opening files not on the SSD. But at idle a hard-drive shouldn't make any noise at all, except maybe a faint whirring up close.
My HDDs are Hitachi Deskstars and they are especially noisy when active, but when idle (but not spun down) they're inaudible inside my Mac Pro. I've never found a Mac Mini drive to be any different, and I would have thought the iMac would be the same; I have two Mac Minis now, with just the stock HDD (so no SSD helping to reduce noise) and I can barely hear them even when they're active.
I'm actually running Mountain Lion on most of my machines so I don't believe so; I have Mavericks on a small partition for testing though.
I just find it really strange you're experience much drive noise, personally I've found the fan inside the Mac Mini to be noisier than a (mostly) idle hard-drive, but even that's not saying much as even under heavy load I wouldn't exactly call the fan noisy either. And I actually have pretty sensitive hearing so even things like minor buzzing from a power adaptor annoys the hell out of me (which begs the question of why my Mac Pro's GPU fan hasn't driven me insane yet, but that's not really important here). I only have an older iMac (2009 I think, don't really remember) but it's usually as quiet as my Mac Minis are, maybe a touch noisier when the disk is under load.
How long did you have the iMac for? It's possible your Fusion Drive was still "settling", but personally I found mine was about right after about a day, and I only have a relatively tiny 120gb SSD (on top of 3tb of HDDs). So most files I open give me audible HDD noise, but when I'm just generally browsing and stuff it's all from the SSD. The official Fusion Drives should be a single 3tb drive with 256gb of SSD I think, so I would thought it would have an easier time.