By default, here are the colors of links from Academia, pulled from the CSS:
The hover color is the red of the leaning book in the logo, which is actually quite noticeable.
Instead of increasing contrast, increasing the saturation by increasing the blue, similar to the cyan that is used in meta, should be sufficient in differentiating the links from the text. Making the text darker and keeping the link the same color, or making the link darker or brighter, will be less noticeable if they are the same relative saturation. It is relatively easier to notice differences in color and contrast than solely differences in contrast.
Also possibly problematic, mousing over a link in Academia Meta makes it turn the same color as the text.
Edit: Does this go to a web developer for Stack Exchange? Do we need to do anything special? I know on Stack Overflow, the web devs literally fix things within seconds. This isn't crucial, but because we have no feedback, there's really no way to tell whether a person who can change this (and it's not a big change AFAIK) has actually seen it <_<