While I'm not someone who is a superfan, I still enjoy a good story, especially when they feature strong, well-written female protagonists. I like the character Felicity, and since it seems as if Naomi is essentially the same, I have a feeling I would like her character too, which makes me want to see her in live-action format. I also am not a fan of killing off female characters to create more angst for the male hero, which was why I cited Gail Simone's Women in Refrigerators trope. (Full disclosure: I'm more of a Batman fan, and Barbara Gordon/Batgirl was my favourite heroine growing up, which influences my opinions here.)
That said, you're right, I'm missing a lot of the context because I am not a Green Arrow reader. So I care, but I'm not really that passionate about what happens to Naomi either -- I would just think it would be a waste to lose her if she is as likeable or important to Oliver as Felicity's CW character in the show. I also agree that having overly similar characters together risks making a hot mess -- hopefully this can be avoided by giving each of them more unique characteristics outside being Oliver's potential love interest and being good with computers.
@statsgirl, that would be interesting too, however, I think overall the general consensus may be correct to assume things aren't looking good for Naomi. It seems that having a smart, competent, female computer expert is like Highlander: there can only be one.