It is a marketing thing. In the GDS tools that travel agents use a "direct" flight will show above connections. In the good old days a direct flight was actually the same plane traveling directly from one point to another with a stop en route. Now the stops often involve a change of aircraft and can result in missing your flight, even though it is a direct flight.

As for credit earned, you only get the point-to-point miles and the one point, not the bits from each segment. CO 6/7 operate from SAT to GUM via IAH and NRT with three different planes. The mileage credit difference is 15%. That's a pretty bad one to book as the direct flight number from a credit perspective.