I managed to plug my charger upside down in to an outlet overnight. Will this have any negative effect on my iPad?

The two prongs on the charger are the same, therefore the charger doesn't require it be pluged into a receptacle in a specific orientation. Either way works. In fact the charger is slightly asymmetrical and this enables you to turn it over should something else be in the other outlet that interferes with the iPad charger.

Polarity might get reversed, but if plugging it back in normally doesn't result in any issues, I wouldn't worry about it.

This is one reason I prefer to use an adapter thtat includes a ground plug. Then you can never mess up the direction.

You're talking about the little two-prong block being plugged into the wall upside down, right? That's not a problem at all. If, OTOH, you plugged the cable into the iPad upside down somehow, I can't imagine that wouldn't cause some physical damage.