Are there any reasons not to include the zest when citrus juice is an ingredient?
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.