There is no reason you wouldn't earn the correct SC and points for these. They are still separate segments, just as with the two segments of the QF flights.I am travelling on the flights below, they are both UA406 but not sold as a non-stop like QF1 SYD-LHR or QF1 SYD-SIN-LHR but I have a feeling VA will treat it as a single flight because of the same flight number.
Minor point but airlines advertise the QF flights as "direct" with one stop, not "nonstop." Nonstop only applies if there are in-fact, no stops at all. Your YVR-DEN service under the same flight number could still be called "direct" under official airline terminology, even though it requires the change of planes at LAX. Note how the availability is the same - it's one fare (similar to a married segment).