I don't have a whole lot to add outside of offering my own personal experience with scanning artwork. I don't think there is much of an issue with putting up non-digital comics online. Do you plan on inking your art? That would make a world of difference when you scan it in terms of clarity. I find my pencil drawings tend to look somewhat washed out when I scan them. Either way I'd suggest you throw them into Photoshop once you've scanned them and tweak the contrast and color.
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