I tried with Keynote '09 version 5.0.3 (791) on 10.6.4 by dragging QT movies from a finder window to a Keynote slide. That copies/embeds the dragged QT movie into the Keynote presentation.
result: aspect ratio doesn't change (16:10 movies stay 16:10)
Using the "Media" palette (near upper right corner of Keynote's main window, 3rd icon from right), appears to work correctly also.
result: aspect ratio doesn't change (16:10 movies stay 16:10)
Using menu: Insert/Choose..., same results.
Hmmm...
The movies you're importing don't happen to be a video format with non-square pixels?
Take Care,
Chris