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It could definitely affect your SEO with the larger engines. They take things like the content's position on the page and the way it is presented to the user as variables in their ranking algorithms. As far as how much it will affect it...there's really no way to know without trying it.
The best approach would be to nest your pages beneath a broader category-type menu rather than listing each individual page on your menu, but this could be a bear to do in Wordpress, I am not sure.
If it comes down to not displaying content vs. being unsure about SEO and displaying it, I would definitely put it out there however you can. Good content will negate any penalties you might incur from content organization.
Hope that helps.
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