This method of structuring navigation is not inherently bad nor will you be penalized for it. There isn’t an automatic red flag that goes up and many sites use sitewide links. The only time Google has an issue with it is when they are following the same spammy tactics displayed by other links that aren’t sitewide. So in a nutshell, as long as you are creating a good user experience and not trying to game the system, you will be fine having these on your site.
Here is Cutt’s explanation,