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Don't worry, your logic is on track.:) Any server side includes are executed before the spider ever sees the page. It won't cause any problems. Many sites handle their meta data in this way.
However, one thing to consider. Using includes for your meta info usually means that you are repeating titles/decriptions across multiple pages, which isn't the best idea. Having titles and descriptions that are unique to the content on each individual page will produce much more traffic.