It does make you a little bit paranoid, yeah
Once the enemy has gotten in there, though, you'll never know how many might be left lurking.
However, the build rate of mobile spaceyards is very very poor when working on ships, so there will never be hordes of enemy flowing out of a nebula or storm.
What I tend to do is build a modest defense net of satellites at all the exits, so when they do come out, they will be crippled or destroyed, and then my local ships can handle the cleanup and repair duty.
The Fetid Nebula in Carrier Battles #2 is a good example. It sits on the border of three races, and everybody has a zillion sats everywhere... except in the east warppoint, where (from admittedly second hand reports) an invasion swarm was halted with major casualties.