I have a recipe for vegetarian Moussaka which calls for red lentils, but it doesn't specify whether these are split red lentils. Is there such a thing as whole red lentils (I have only ever bought split ones) and will using split red lentils instead, confuse the measurements in the recipe?
They are not the same, there is a difference. Red lentils can be purchased whole or split. Most red varieties are skinless, those that do have skin don't appear very red.
The measurements aren't going to be affected much, you'll get slightly more lentil in a cup of split lentils than a cup of whole lentils. The cooking time will be more dramatically different. Split lentils with the outer skin removed will cook faster than whole lentils, particularly those that still have the outer skin.
I looked at a few recipes for Moussaka with lentils, and they all called for cooked lentils. So whatever lentils you choose, follow the instructions on the package or your knowledge of the product.
Whole lentils will maintain their shape more (although the red varieties won't stay whole), split lentils will break up more. Which you choose should be a matter of personal preference.