1. When there the two flights with the same number, the 2nd one will have number 5xxx for air traffic considerations.
2. For Int'l-EWR-Domestic one-stop, yes, it means absolutely nothing. And since you'll still have to get off, go through immigration, collect luggage, clear customs, recheck luggage, and reclear security anyways.
3. The only one-stop flights that constantly use the same equipment is CO51 EWR-IAH-EZE on a 762. [But the 1st leg, FRA-IAH is on a 764.]
4. Careful when you book a "direct" flight as you only get mileage for the distance between the first city and final. You may be cheated a lot of miles. [For example, IAH-EWR-PEK, or SAT-IAH-NRT-GUM, for example.]