It does not affect to SEO only if you're using for legit purpose.
Bad practice always heart SEO, it does not about whether you got penalize or not.
For example, you got chance to write some article on quality website, but you're placing links with inline CSS so moderator don't see it, then it is consider as bad practice. But if you do for legit purpose then it will not heart, just make sure you don't manipulate them.
You should note that all links does not add same value, links that are useful for users may pass more value than others. For example header pass more value then body links, and body links pass more value than footer links.
It's all about whether it is useful for users or not. Google may treat all links same at this time, but once they got understand your site, they may treat them separately.
My personal advice is use some hover effect or use underline text decoration style in links.