Yes and no.
There are a lot of variables to consider. For some cards and for some buyers - yes, the fact that the card cant be hand-held and condition is somewhat "suspect", it can indeed reflect in the price. I think the bigger drag on prices due to eBay comes from the increased supply that you wouldnt necessarily have available otherwise. If you're searching for a card that can be found on ebay, chances are it can be found multiple times and easier than you would at brick and mortar stores.