I’m afraid not, anonymous. Missing limbs or other body parts, as well as major scars, generally don’t repair themselves as a pokémon evolves. Scientists are admittedly not sure why this is so for scars, especially as an evolution quite literally transforms the body into something new and stronger, but for limbs and body parts, it’s a pretty simple explanation: you can’t transform a body part into something new and stronger if it doesn’t exist.
Don’t worry, though—nowadays, there is a lot more acceptance of pokémon with disabilities such as those, and there are plenty of resources to help you and your croagunk train without being hindered by her lack of an eye. The biggest piece of advice I can give you at the moment is always support your croagunk (or toxicroak) and reassure her that she’s just as strong and capable as fully able-bodied croagunk and toxicroak.
Best of luck!