Is this in a Twitter app, or in Safari?
Twitter apps, both original and third party often have several themes. I use Tweetbot, and it's fairly easy to change themes by accident. All it takes is a two finger swipe up or down.
If in Safari is it specific to a site, or on all sites?
Sites, like apps, can have themes. There should be a way to change them in the site's preferences (on the site).
If the change is universal throughout Safari, and probably in many other apps, you may have changed some of he Accessibility features. I don't remember where to find those in iOS 10, but they should either be their own group of settings or hiding under the General settings.
The Safari app itself does not have a setting that will change the link colors. There may be ways to temporarily change those colors, but forcing Safari closed and opening it again should stop that. Or, just power the iPad off and on again.
