Is SOL the only place ships can be built? Are there other systems that have bases that can build ships? Are there modules and stations that can build ships? I am finding it very difficult to get too far from Sol, mostly because my bases and mining facilities keep getting destroyed. I'm trying to find away to set up a new HQ far away--but I really can't, since I have to come back to Sol to make ships and stations.
Make SOL your base. Put some science-dedicated ships in orbit--also for manufacturing.
There's no real need for a base, unless you're mining a prospector mission. Is that what you're doing?
Supernovas did make mining harder. I've adapted by using a ship to defend the station/planet. This way if I forget to evacuate, the supernova will only destroy what's on the planet and what's in cargo and the cargo modules. What's on hte ship is protected, including all of the combat modules. And another reason to do it is ships receive a large power bonus, I think. I've also put some Solar Infusers on it to (hopefully) slow the aging of the star (and get some fuel cells too).
The whole "everything on a station or planet is destroyed in the event of supernova or attack by other players" needs to be looked at and considered in context to ships. Ships cannot be destroyed. I don't feel encouraged to build up defenses on stations/planets. For that, either the bonus needs to be much higher, or the modules need to be partially protected.
EDIT: So what you're doing is putting some random miners on planets outside the inner rings and putting stations in orbit and supernovas are destroying them? My advise is to do prospector missions and focus on just one base at a time. For that you need to make a ship suited for SOS missions. Otherwise, if you're putting science labs on planets, don't. Put them on ships and put those ships in Earth orbit. They'll remain protected indefinitely. With the amount of module space on a titan and by researching science labs, you'll find you'll never have enough money to maximize research.
Here's another idea... Make a COM ship and when you're doing it, deploy miners. When the COM is over, collect the miners.