I have used iPhone since OS version 2.0.0 on my iPhone 3G purchased on release-day in July 2008, and I can tell you that Safari on my phone has never, ever, ever done this, and I've never seen any other iPhone or iPod Touch on the planet across all generations and versions of the OS that do this, either. I've got an iPod Touch that I've used all three generations of OS on (1.x, 2.x, 3.x), and it has never done what you describe, nor have any of my other friends' iPhones or iPod Touches (and I've had many pass through my hands).
Mobile Safari will try to render the page as faithfully as it can, assuming a static screen size. Unlike the browser on your computer, which will, in certain circumstances (depending on whether the HTML/CSS is coded on that page or part of the page for relative screen sizes or for static widths defined in pixels), reflow the text if you resize the browser window, Safari on iPhone picks a certain screen size (width) to emulate and sticks with it. As you zoom in and out (however you do it...pinch-zoom or double-tap, it doesn't matter), or even rotate the screen, the specific "width" of a given element doesn't seem to change and the text never "reflows" to fit a different element size. The effect is more akin to a newspaper article that you take a magnifying glass to. You are simply zooming in and out, not changing the amount of space that the text has to live within. (This is why the double-tap gesture is so powerful, and why it exists alongside pinch-to-zoom: it automatically zooms in just enough to make the text element you are looking at fit the exact width of the screen, so that you
don't have to scroll side-to-side to see all of it.)
So, I really don't know what to tell you. I don't want to say you were imagining things, but...maybe you were imagining things?
In any case, even if you weren't, there's no way that this would be a 3G vs. 3GS thing. Mobile Safari is the same code on both phones. This would have to be a software issue. If something changed, it would be between OS/firmware versions, not between devices.
-- Nathan