If you bought a T3 Excelsior or Nebula then yes, you bought them with ECs. That was the only way you could buy them when they were introduced into the game - and they were EC purchases per character, not per account.
I didn't. I bought the Long Range Science Vessal Retrofit (Voyager) and the Tactical Escort Retrofit (Defiant) with Cryptic Points. When I buy a ship, I want all of my characters to have access to it and I wanted to support the game. Two of my characters still have them in their inventories, but no one else can access them.