I am starting to think Cryptic is treating starships like powersets in Champs Online. I believe from Cryptic's perspective, they are not just selling players a model but more importantly they are selling you starship "abilities". Buying a certain ship gives you a certain subset of boff abilities to choose from as well as a single "special" ability in the form of a console.
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.
On a related note, lifetime subscription costs probably $300 because Cryptic believes the average lifer will play for 2.5 years/30 months/912 days. This could explain why they are stopping lifer rewards at 1000 days (oh what the heck, 900 isn't a nice round number so lets give them one more reward at 1000 days as a bonus) Coincidentally, this works out to be exactly $10 per month, about the same as what a gold subscriber would pay in the same 2.5 year period. Using these figures, a $20 starship is equivalent to 2 months of subscription which means Cryptic needs to sell you a ship every two months.
Of course, all this is just my speculation. Take it with a huge dose of salt.