Boom
I got nothin'
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Yoji Shinkawa speculated that Liquid Snake did have darker hair at one point - but long-term exposure to intense sun rays in Iraq had bleached his hair (think Tom Hanks in Cast Away). That's always been my preferred explanation for Liquid having blonde hair despite expressing Big Boss' dominant genes. But then again, is sun-bleached hair permanent? Liquid was rescued from Iraq in 1994, so there's an eleven year gap between his rescue and his insurrection at Shadow Moses. If sun-bleached hair isn't permanent, then his hair would've grown out normal by then.
As for Snake's hair color, the original plan was for Snake to be blonde - at least while disguised as Iroquois Pliskin:
This concept got as far as initial testing, but was ultimately changed because the testers thought it lacked association with the Solid Snake we saw in MGS1. However, Pliskin's hair color is noticeably lighter than Solid Snake's in the final game, so perhaps this idea was still implemented to a certain extent.
And here's another fun fact about MGS2. The game was originally going to be cell-shaded, because Kojima wanted the game's visual style to reflect the concept art. Here's the beta Solid Snake:
As for Snake's hair color, the original plan was for Snake to be blonde - at least while disguised as Iroquois Pliskin:
MGS2 Script said:The man pulls off his balaclava with one hand to reveal a head of blonde hair and the face of a man in his 50’s. His face is stubbled; there is no bandana is sight. His appearance approximates that of Liquid Snake in the last title. Raiden continues to stare him down.

This concept got as far as initial testing, but was ultimately changed because the testers thought it lacked association with the Solid Snake we saw in MGS1. However, Pliskin's hair color is noticeably lighter than Solid Snake's in the final game, so perhaps this idea was still implemented to a certain extent.
And here's another fun fact about MGS2. The game was originally going to be cell-shaded, because Kojima wanted the game's visual style to reflect the concept art. Here's the beta Solid Snake:


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