I suspect that certain traits were more common in the different courts before the civil war, but these were not as pronounced as in the Age of Rebirth. I always assumed there was intermingling before the civil war, and that their appearances still aren't as different as the stereotypes would suggest. After all, the Ljosalfar leader Thessa is fair skinned and dark haired (judging by her leader pic), and Amelanchier doesn't look like he is blond either (although his hair is hidden).
The differences are more political/ideological than genetic. I don't think an elf with an overtly Svartalfar ideologies/philosophy/political leanings would be welcomed in a Ljosalfar village, and a Ljosalfar or an elf sympathetic to Arendel wouldn't live long among their sinister cousins. Traitors from either court might be welcomed among their old enemies though, and the Svartalfar would certainly try to plant spies among Arendel's people.
There are also other groups of elves that aren't really tied to either court. Although not presented in the game, I believe Kael has said that there are many isolated independent groups of elves with no loyalties to either court. Some may have picked a side since then, but other might be open to both groups and interbreeding between the non-aligned elves and those loyal to both queens might still happen.
Other groups of elves were so isolated that they never knew either court ever existed. These include the Once-Elves like Varn and his family, who were enslaved by Laroth in the underworld and then escaped to found their kingdom in the sunless Shadowed Vale. These are specifically stated as being no more closely related to the Svartalfar than the Ljosalfar, but their environment lead then to be dark haired and pale like the Svartalfar. I suspect they probably even more Svartalfar-looking than the Svartalfar, since the Dark Elves were just nocturnal but the Once Elves lived their whole lives without sunlight, moonlight, or starlight.
(Not particularly relevant, but the independent elves that worshipped Bhall changed even more. I believe these are now called Goblins)