Firstly, going the CSS route with less HTML markup and nested tables dramatically increases browser rendering times for the user. As far as search engines are concerned, search engines do take into consideration the file size of each page they access. They will limit the number of bytes that they download per session so as to not allow googlebot to take down a server spidering an entire site in one session. Additionally, they will only index the first 100KB or so (not sure of the exact number, but something like this) of a page. HTML markup takes up a lot of kilobytes. There is evidence in this in the Google Webmaster Tools, where Google now allows you to see graphs of the number of bytes download per day, and temporarily control the rate at which googlebot can spider your site if you have enough bandwidth to spare.
Additionally, search engines put more weight on the content which appears closer to the top of the page. Suppose you have a two-column table where the left column is a sidebar and the right column is the main content. The left column (the sidebar navigation) will always appear first in the HTML markup, giving the navigation slightly higher importance over main content. With a completely CSS layout, you could use fixed positioning to put the markup for the left column below the markup for the right column in the (x)html code, thereby putting the higher prioritized information closer to the top of the page.
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