the bullet hole is still there when the camera is outside the car, if you look closely, the crack in the windshield is still there and the hold is right around where Arnie's hairline starts so it's a little hard to see, but it's there. The time it does dissapear is when John or Sarah asks Arnie if he can "see" after he turns the headlights off, and it show's his "vision" working (scanning the road) and there is no bullet hole in that scan.
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In response to EC: I don't remember if this is stated explicitly in either movie, but the Terminator is a Model 101 of the T-800 series. I know the script refers to the metal skeletons at the beginning as Series 800 endoskeletons, and I think the first teaser for T2 - the one with Arnold on an assembly line - has something like the words "T-800 SERIES, MODEL 101" on a computer screen.
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