When you have lost a ship, you can easily rebuild it by pressing the number key associated with that hangar (providing you can afford to rebuild it ).
There is also an auto-rebuild function in the Hangar View (F3).
Keep your fleet at max size whenever possible.
Try outfitting your ships with different weapons for different situations.
If you simply can't afford to build any more ships, you can always revert to the basic Short Bus design free of charge.
