Well...the hood would certainly affect the way the amount of light that gets to the lens. But in the absence of glare, all it's really doing is cutting the light. As maxharvard points out, it's for glare, not for metering. In other words, the lens hood isn't a way to control the exposure. If one image is brighter than the other, all you're really talking about is exposure. Most landscape photographers prefer full manual. If that's a little scary for you, learn EV compensation...and learn your metering modes. Shooting a landscape like that, you'll want to use center-weighted (dot and donut icon on the Nikon) or evaluative (filled box including dot, donut and corners on the Nikon). But never fully trust your meter.
My advice, you should keep your hood on most of the time anyhow. It doesn't hurt the shot, but it will block flare when necessary. If nothing else, it also protects your lens.
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