Defense in depth for me. I pretty much know that even the most heavily fortified chokepoint world I can reasonably get in the early to mid game is probably going to leak some exo ships, especially the stronger ones. I keep a good amount of defense on my homeworld no matter how far out the "border" of my "space" is, because of this. And it has saved my bacon on multiple occasions (and I guess the last remnant of human civilization too, but mostly I was defending for the bacon
)
Also, having some tractor turrets grav turrets on your own core worlds, both in from the "outside" and the wormholes to your HW help greatly. Your own core worlds also make great places for black hole generators if you have the trader turned on.
And finally, forcefields. Tons of forcefields.
I use them both to protect the important stuff and over wormholes I want to stall them getting through (again, like your own core worlds over the wormhole to your HW)