I have recently discovered a much broader use of lemon juice in my cooking and now add it to almost all stews and soups a few minutes before the end of cooking. But I am curious if there are benefits to adding it earlier, e.g. if it will cook in better and give it a zestier flavor if I cook it longer than just adding it at the end of after. One example that comes to mind are fava beans, which are great zesty. The downside of cooking lemon juice is that it can cause undesired curding of some vegetable protein.
Cooking lemon juice longer won't make it "zestier." Like most foods added in small quantities as flavor enhancers, lemon juice has a lot of aromatics and flavor components that could boil off, break down, or get absorbed by your stew/soup with longer cooking.
There's a reason why a fresh lemon or lime slice is often served beside a lot of foods (and drinks) -- you'll get a stronger lemon flavor when it is added fresh at the end of cooking. A splash of lemon juice added earlier will just give a generic acidity to a dish; you might as well use vinegar or any other (cheaper) acid.
The only reason to add it earlier is in a dish where you use a lot and want the lemon flavor to penetrate the dish fully. But in that case I wouldn't tend to use plain lemon juice but perhaps more of the actual fruit. Rinds can be bitter, so you could add zest or chopped up peeled lemon pulp, but lemons are sometimes a bit of work to peel and remove seeds. A better option for this application is preserved lemons (i.e., lemons added to salt and kept for long storage), which can be chopped -- rind and all -- and added to stews earlier in the cooking process.