If only the Simulator shows those artifacts, then by all means ignore them! None of your users will ever run your app in the Simulator, will they? The Simulator isn't perfect.
A spacing of 2 pixels around each texture atlas sprite frame is enough (and generally recommended) to kill all artifacts caused by pixel bleeding. If you still see artifacts, they're not a direct cause from too little spacing. They can't be.
I'm not sure about Zwoptex, do you actually have to manually create each scaled-down version of the texture atlas? You may be doing something wron there. Try TexturePacker, I wouldn't be surprised if the artifacts go away just like that.
For example, one type of artifact is caused by not placing objects at integer positions. You may see a gap (usually a black line) between two objects if their position is something like (1.23545, 10.0) and (41.23545, 10.0). Using integer coordinates (1,10) and (41,10) would fix the issues. The difficulty is that this goes all the way up the hierarchy, if these object's parent node is also on a non-integer position you can still experience this line gap artifact.
If you search around you'll find numerous cause and effect discussions for cocos2d artifacts. One thing to keep in mind: do not use the CC_FIX_ARTIFACTS_BY_STRECHING_TEXEL macro. It's not a fix, it doesn't even come close. It kinda fixes the non-integer position artifact and introduces another (much worse IMHO): aliasing/flickering during movement.