Google’s Gary Illyes said in an SEO office hours video that having multiple navigation menus will have no impact on your SEO performance. That means no positive or negative impact on your SEO performance.
The question came up at the 10:05 mark in the video.
Question: Can having multiple navigation menus hurt SEO performance? A main menu with all the most important categories of the site and the secondary menu to enhance categories related to brand extensions.
Answer: It’s highly unlikely that having multiple navigation menus will have any effect whatsoever on your site’s SEO.
There you have it, it doesn’t matter for SEO purposes to have one, two or more navigation menus. Google is probably able to figure out that you have your navigation on the top, left and bottom of your page.
Here is the video embed:
Forum discussion at Twitter.