Will my website be affected or penalized if it has unnecessary links in its footer section? The links are already present on the top of the website.
It does not really matter unless you have a thousand internal links in there. Just make sure you have an adequate amount of external links pointing to your domain and you will see the result.
A couple of years ago I was hit hard for having too many internal footer links. Beyond the obvious ones — Home, Main Pages, and the like — you run a risk of being penalized for "footer spam." Since then I've simply put my main navigation links at the top left, for example in this page from my website — http://www.jimfeeney.org/comforting-words-distress.html — and keep the footer links as minimal as possible.
Don't worry about that. If link is relevant to your blog it's OK. Matt Cuts, head of google spam team, said that 100+ links per one page doesn't means that it's spam. Content and links must be relevant.
If you already have the links on top, why have the same links in the footer. Even if doesn't mean a penalty for you, do you actually gain any benefit from them? After all, you have to think about user experience too, so repeating something all over the place might not be your best bet. Further more, as mentioned, too many links in the footer is definitely a risk so be careful about the number of connected pages you have there.
I can't see how you would be penalized. What I would worry about is where are those links pointing to? If they are pointing to questionable sites, then you may want to remove them. However, if they are just pointing to "safe" sites, then what's to worry about?
Well, OP mentioned it was about internal links only, so this should be out of the question. Still, I would refrain from doing it in large quantities, simply from the User's perspective. Maybe put the most important few sections to link and that's that
Here's a terrific article on footer links/spam by the well-respected SEO Jill Whelan — http://www.highrankings.com/footer-links-349
An excessive number of footer links with keyword rich anchor text would be viewed as spammy and can get you into trouble. This is something that was done a lot in the travel sector. Do stuff for your users not for SEO. Obviously it's fine to link to the homepage, contact page, etc but is it really necessary to include every internal page in the footer navigation? Probably not.