Eh, no. They did not discover that mining sites are being placed in deep locations. They discovered that whales visit those locations because they dive deeper than thought.
So maybe: "Deep diving whales may cause licensing issues for prospective mining sites".
The use of the word "that" and the lack of a comma means that "that whales visit ..." is a restrictive clause. Contrast with "placed in deep locations, which whales visit ...".
The phrase is ‘deep locations that whales visit’. My intent was to phrase it in a more precise but not necessarily more poetic way.
I think the issue is that the mining sites are going to cause issues for whales, which in turn causes issues for mining licensing, due to the environmental portion of regulations. The whales were there first, and your version again inverts the main topic of the article, which is actually beside the point.
So maybe: "Deep diving whales may cause licensing issues for prospective mining sites".