You might get more dirt in the engine bay/fenders but as far as rusting all of the Nissan genuine components are guaranteed against rust. It shouldn't be that big of a deal anyways since you mentioned only cutting a small section out and leaving the majority of it intact.
How low did you go anyways? Are you on stock wheels and tires? I'm running super low on a Nismo (about 2+ inches lower than stock) and I haven't touched my fender liner. I am running a few clicks from full stiff on dampening though.
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