Mmm there is a way but it involves bring up the console make sure you click on said item to be destroy first use ~ to bring up the console then type in destroy and hit the enter button.  Alot of work if you ask me!

yea I too would like a way to remove older ships out of my inventory. 

"Remember back on those old Ranger mark I's? Well we used to use old microwave ovens pointed out to space for our shields! Nowadays they use the improve Nova-star field generator!" 

Yea we need a way to remove old starbases or ships but i am sure this will come later.