will unhatched eggs in incubator affect good eggs?

Sounds like it has been a learning curve for you. The odds are tremendous your next venture into incubating will be less stressful. I know my second try was less stressful.

As far as removing the eggs. If they are not rotting, it will not have any bad effects to leave them in there. The only problem is that they might explode and get that infected-with-microbes stinky stuff over everything, including the good eggs. If they don't stink when you sniff them, they are probably pretty safe. As long as they don't stink, I'd leave them in for several days after their due date. If your incubator is running a little cool, they could hatch a day or two late. That happens all the time.

Once you are sure they will not hatch, there is nothing all that bad about taking them out. The eggs in there help give thermal mass. That means when you open it to add water, candle, whatever, or you get a bit of a temperature spike, the incubator tends to take longer to change temperature. It keeps the incubator a bit more stable. I think the risk from an egg exploding is much worse than this loss of thermal mass, so I would suggest taking them out after they are maybe 4 days past due date, but if they are not stinking, it probably does not matter one way or the other.