can they find underwater craters? they seem quite certain about the yucatan one despite it being 100x older. I would assume a relatively new crater filled with sediments would be something that would show brightly on those ground radar things they use. I am hopelessly ignorant about this though.
Any number of clues can reveal a “drowned” crater. However, as the article speculates, volcanic activity could cover or envelope the evidence.
Then again, we should be able to detect and date past volcanic activity fairly accurately...