Do I always get an upgrade I purchased? So if I upgrade a ship now and melt it later, can I get the upgrade back?

If you melt down an upgrade separately (i.e. do not use it) you will be credited with the corresponding credit value on your account and can also buy the upgrade back from the buyback list if necessary. 

Once the upgrade has been applied and the upgraded ship is melted down, you can only buy back the base ship (i.e. the original ship without any upgrades applied). You will receive the full value of the upgraded ship, but you cannot buy back the upgrade separately.