Yeah, but I think people would be smacking their heads if they were ready to explore the Galaxy for a new system to colonise, and then realise that every system they find near their Homesystems is Planetless! 8O
I admit that such a scenario would be in the realms of near-impossibility, but could you imagine it? You wouldn't even bother playing the game, you'd just start over! 8O
Besides, there is empty space to create 'barriers' to expansion - you may find many large areas without starsystems, which you'll have to cross before you can find what hides on the other side. You never know, you'll find that all-important minor race that turns the tide of enemy spies or gives you the extra edge in research capability that you need to beat your enemies.
I don't think you need to have 'empty' systems because of this.