Considering the sensitive nature of this ship, will purchases of this ship be limited in game, like by reputation? Does the UEE try to prevent ships like this from falling into pirate hands?

With the 2947 announcement, we consider the Eclipse to now be 'for export,' meaning that it can be sold to select groups outside the UEE military (including you). We anticipate there will be any number of limitations in the game world including both the number of bombers produced at any given time and other factors relating to reputation. It seems unlikely that the UEE would sell bombers directly to known pirates or other criminals, but it's also easy to imagine other ways for such individuals to acquire military spec'd ships.