Which game is harder to Nuzlocke?
Black 2 and White 2 are generally considered some of the hardest games in the series for a Nuzlocke, thanks to threats like Clay's Excadrill, Ghetsis' Hydreigon, and Iris' Haxorus. In general, Trainers have stronger Pokemon with more competent movesets than HeartGold and SoulSilver, which makes planning fights trickier. I recommend Iridacea's excellent guide here.
When does a Johto Nuzlocke typically officially end?
The Johto games are unique among Nuzlockes for not necessarily ending once you enter the Hall of Fame. Many players consider beating Red to be the end of the game—though you could of course go for a more traditional Nuzlocke, ending at Lance, and no one would stop you.
Which one generally has better encounters?
Black 2 and White 2 have a higher power level across the board, making it more likely that you will get something strong from every encounter. Guaranteed encounters include Emboar, Zoroark, Sawsbuck, and Jellicent.
HeartGold and SoulSilver, by comparison, have encounters that are weaker on average but still able to meaningfully contribute. Guaranteed encounters include Feraligatr, Gyarados, and Fearow, with other strong Pokemon like Graveler and Crobat being highly likely as well.
Which is more fun?
I believe Black 2 and White 2 are more fun because of their higher power level, more engaging level curve, diverse boss battles, and greater movepool flexibility. I find HeartGold and SoulSilver to be a bit of a slog with six Pokemon thanks to their subpar level balance—this problem is mitigated in Black 2 and White 2 with better game design and the omnipresence of Audino.
Ultimately both sets of games are enjoyable Nuzlocke experiences (but you should totally play Black 2 and White 2 first).