Does the size of the pepper have any affect on how hot/spicy the pepper will be? ex. Is a smaller ghost pepper less hot than a ghost pepper twice its size?
As an overly broad generalization, yes, smaller peppers tend to be more spicy.
To answer in more detail, the heat in peppers comes from a molecule called capsaicin. The concentration of capsaicin is what determines how spicy peppers are relative to each other.
Incidentally, this is also how spiciness can be measured. The Scoville Scale is a measure of how many times you need to dilute the pepper's capsaicin before it is no longer detectable by taste. While this is subjective, it's a decent point for comparison between different varieties.
Larger peppers like bell peppers or banana peppers are low on the Scoville Scale (0 & up to 500 Scoville Heat Units respectively), while smaller peppers like Serranos (up to 25,000 SHU) and Habaneros (up to 350,000 SHU) are usually much hotter. Thus you have a trend with smaller peppers being hotter.
NB: Scoville units per pepper listed as 'up to xx', as there can be huge variations dependent on things like soil composition and climate. This is why you can get some Jalapenos that aren't terribly spicy, but then get others that are (relatively) really hot. SHU listings from Wikipedia.