You can get 3 master balls in soul silver and heart gold with using the 999 master ball cheat. I DO NOT know the cheat code.
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In Pokémon HeartGold and SoulSilver, the PokéBalls that you can get are: Poké Balls, Heal Balls, Great Balls, Net Balls, Dusk Balls, Friend Balls, Level Balls, Moon Balls, Heavy Balls, Lure Balls, Fast Balls, Luxury Balls, Ultra Balls, Love Balls, Nest Balls, Premier Balls, Quick Balls, Repeat Balls, Safari Balls, Timer Balls and Master Balls.
There's no such guy in Sandgem Town that has 3 Master Balls.
in heartgold master ball.in soulsilver bring a water Pokemon and use a water type move on it.then use a ultra ball.bring lots of ultra balls and dusk balls.
at cinnabar island there is a net ball 5 master balls in the hidden chamber (you need hidden power) and last but not least 5 timer balls!not sure but I think after you beat the league Kirt will use two different apricorns
with action replay you can get 999 master balls