And every time you use a boff ability, you're really using a small amount of Cryptic's server. I'm guessing they've calculated the average number of time boff abilities is used over a period of time and figured out how much it costs to run STO servers and pay developers for that period of time. And that gives them a baseline cost of how much ships need to cost in order to run a profitable service.
Nah. That's not how they price things like this. Cost is minuscule when you're dealing with intangibles like this. Pennies per ship per year. The price floor is set by the man hours it takes to develop new content plus an acceptable margin for shareholders. Mind you, that's the floor, what the price might be during sales.
When they're setting the standard price for new items they base it on what has and hasn't worked in the past. Basically, price it at what the market will pay. They pick a balance between price per unit and number of units sold (x*y=z, where z is maximized) and that's what they price things at.