You can change your ship designs when you already have ships of that type flying around.

Simply go to the ship design screen and change an existiing ship's design.
eg. add or upgrade weapons. etc.

But watch out! Any upgrade will cost you the difference of your change multiplied by the number of ships you have of that type.

If you try to confirm the change and it just won't work: You have not enough money!

But having enough money you can upgrade your ships any time.

You can even use this as a tactical strategy:

Let's say you are loosing a battle right now.
Quickly pause the game and add some repair (or self-repair) units to your ships.

Or if you are about to lose your whole fleet, just rip out all the weapons and addons to get back that money.

Another thing you can do with this: At the start of a new game, sometimes you get some space-stations for your planets. Simply go to the ship designer and remove all weapons and shilds from the stations. Stations suck! But the money can be very useful.

With this trick you can build a large fleet of strong ships for a low price.

This works best if you already have some ship tech researched and several planets with shipyards.

1. Go to ship construction screen
2. Create a new ship design (or modify an old one)
3. Just select the base size (for intermediate gameplay the middle sized ones are the best, below Titan)
4. Remove all weapons, shields, addons, anything - i think you need engines though - SAVE
5. Now go to your planets with shipards and add the contruction of several of these ships - they are cheap and fast to build
6. After you queued them (before they are built) go back to the ship construction screen and add all the weapons and addons you like

You will not have to pay anything extra and the construction speed will stay the same as before.
Thus you will have a super strong and cheap army in almost no time.