500% sounds like you had these ships in service for a long time with a lot of tech development since then. Upgrades at that point can be expensive, but it CAN be worth it if you have an elite crew on the ship.
Check the "Grade Bonus" on the fleet display, if it is really high, you may want to invest in the upgrade, just to keep the crack crew around. That crew grade makes a HUGE difference in weapons accuracy.
The other use for old ships is to park them over planets demanding protection. The population is too smart, so they don't care if the system defense fleet is ancient, only that it is there.
Scrapping a ship does break it down to components, and once they are in the stockpile, they can be scrapped for actual minerals. So if your looking for the minerals back, its a bit long to do, but it does work.