The argument against the minimum wage is in the realm of deductive reason and not something you look around for proof of or proof against. It's basically the economics equivalent of 1+2=3. If there are problems with that equation we need to analyze it in its' space and not look around for cases when we think 1+2 != 3. The problem with verifying laws of economics is that we don't know what we're seeing the effects of in reality. Cultural, weather, moods, government policies, etc. could impact what we're seeing in data without it being clear why or how. Empiricism can inform our analysis or can give us new routes to inquiry on but it can't be used to argue for or against the laws of economics as we understand them. I'd avoid reading economic studies of anything for this very reason.
Regarding the second half of your comment, it's certainly true that there can be confounding variables, but I think avoiding empiricism does far more harm to reasoning than relying upon it. There is an infinity of internally consistent models. Most of these will have nothing to do with reality. In order to tell which actually represent the world we're living in, we need to look at the world. Intuition alone has proven a poor guide in most other sciences.