When following a recipe containing "juice of a lime [or lemon]", I can't help but find it wasteful to just squeeze the fruit. Usually, I'll include the meat of the fruit as long as it doesn't mess with the end result. Are there any reasons why I shouldn't just always include the zest as well as the juice to minimize waste?
Can't comment on the nutritional side of things, but the main reason I can think of for not always including it is that it has a slightly different flavour. A much more intense lemon flavour is provided by the zest while the juice has the more tart elements (and of course water).
If you're just interested in avoiding waste, you can freeze the zest.
Sometimes you're using the juice for its flavour, and in those cases assuming you're fine with the solid material in there, it can make sense to add the zest. In other cases, like in making paneer, the critical component is the acid content of the juice to carry out a chemical process, rather than its flavour.