TBF, you really should read get the Musson book and read a coupe of chapters esp. the one on actually building. It will save you a lot of time and trouble.
Spoke calculators shouldn’t include the length of the nipple in the spoke, they should ask what length nipple you intend to use and then work with that. As above, 12mm is standard.
You can get away with using measurements off the internet for hubs if they are sometthing common like a Hope although you really should measure your own as there are a lot of rubbish measurements posted on the internet. Always measure the ERD on the wheels yourself, there’s plenty of potential for variation between rims.
Reasons for doing all this: You *can* get a wheel out of any old spoke lengths within several mm of what you should have, but the closer to ‘right’ you have the easier your build will be and the closer dish will be to what it should be before you have to spend hours truing and dishing.