Wish I could answer that definitively. 
Hardware and OS updates released after the applications always have the potential to be problematic, and I wouldn't say your experience is totally unique, but we don't have the kind of volume of posts that I'd expect if there were an across-the-board problem with new iMacs or 10.8.3. There are certainly issues with Retina displays, but I thought they were limited to poor quality of display, not performance hits. You might want to search here, or Google, for keywords iMac, slow, InDesign, and 10.8.3 and see waht other threads have been started.
Just for laughs, turn off Mail to test...