Does choosing not to submit GRE scores look bad (particularly for CS PhD programs)?
I would assume, but can't guarantee, that if they have a policy that GRE scores are optional then the policy would preclude assumptions about missing scores. So, in that sense you are probably safe.
But, you can hardly control for what an individual committee member might have in the back of their mind.
It might even be possible to learn more about the policies used and how interpretations are made in such cases.
Since some places now make them optional, some students choose not to take them, I also assume. And in the US, at least, admission is based on a wide variety of things, of which test scores are only one.