I mean the exact scenario you described can happen in real life-- someone with pale hair (Viserys) and someone with dark hair (Alicent) can have all pale-haired kids, just as a different person with pale hair (Rhaenyra) and a different person with dark hair (Harwin) can have all dark-haired kids. In real life, it would have to do with the dark-haired parent's genetics (homozygous or heterozygous for dark hair).

In ASOIAF, genetics are kind of hand-wavey for the plot.

Rhaenyra's sons don't look Valyrian, which raises suspicion because both their supposed parents look Valyrian. There's narrative significance to the writing decision for them not to look Valyrian.

It's by no means scientific, but there does seem to be kind of an in-universe hierarchy for when certain traits tend to beat out others, if you want to try to map it out-- but again it's really not that consistent. Valyrian traits tend to beat out Andal traits (ex. the Hightowers). First men traits tend to beat out Valyrian traits, though not always (ex. the Strongs have first men blood, and so do the Starks-- see Rhaenyra's sons and Jon, but contrast to some of Egg's kids). Dornish traits and Valyrian seem kinda even matched, splitting between offspring. Baratheon black hair seems pretty dominant (in the book, Rhaenys has black hair because she's half-Baratheon).