If the option is auto loading (and in pippin’s code they are) then there isn’t any difference except for coding style as all auto loadable options are fetched together in one query in init time and cached in the memory and at this point get_option is not more then a wrapper around accessing a php array.
If you decide to use not auto loading option it becomes a question of how are you going to use the data, if mostly to get the info for a single term then having a multi dimensional array that will bring info about other terms is a waste.