Well, since ZUN forgot to tell the author of CoLA that Marisa's eyes are gold and he drew them as blue...
We now know that Marisa's natural eye color is blue and they turned gold from magic over-use and its a early sign that she might be becoming a youkai like Patchy and Alice.
Patchy and Alice deliberately turn their eye color back to their original colors, violet and blue, when they are not fighting.
Marisa doesn't bother, probably for the same reason she rarely wears makeup. She doesn't give a shit.