I'm going to guess that it's referencing Zion in a Rastafari way (not a Zionist way) - she was in a relationship with one of Bob Marley's sons back in the day.
Lyrically, it is a tribute to Hill's oldest son Zion David Marley, to whom she gave birth in 1997, during her relationship with Rohan Marley.
i guess the question is why they chose to name their child zion, but the zion metaphor in rastafarianism in my limited understanding is an aspirational one of seeking a homeland after a forced exile, whereas israeli zionism is a settler-colonial philosophy similar to american manifest destiny or german lebensraum.
i forgot about that song and it's the same name with the similar meaning; but very different things.
lauryn hill sang about a dream of collecting all of her people somewhere whey they can live out their lives happily & peacefully.
zionism, in the context of isreal, is still collecting your people somewhere but using any means necessary to do so; including genocide; bribing; war; etc.