It costs nothing to store a ship. Other than the fact that you have to buy another one to store your existing ship that is. There's no ongoing fee for storage.
It doesn't matter what ship you're storing. Or how many of them you store. I have several ships now, some the same for different purposes. Exploring Cobra, fighting Cobra etc...
Think about where you're storing them, which means think about where you're buying them. Try and make it as convenient as possible for you to get them back. Most of the time this isn't possible however so you end up with ships all over the place.
In order to get a ship and bring it to somewhere you want it you have to go to the place the ship is stored and then store the ship you few in on, swap to the one you want and then fly that back to where you need it.
Lets say you have two ships. A and B.
Ship A is stored 30ly away. Ship B is the one you are in now.
If you want A and B in the same place you need another ship. So you go to the Shipyard and buy a Sidewinder and store your current ship, B. In your Sidey you fly to the location of Ship A.
When you get there you can then store the Sidey and swap into Ship A and fly A back to the location of B. Or, once you're back in Ship A, sell the Sidey to recover most of the money and then fly A to B's location.
The first way you end up with a new Sidey where A used to be and you have A and B in the same place. The second way you end up spending about 10% of the cost of a Sidey to get A to where B is.