It's pretty clear from a strategic point of view, something that veterans of the Crusades and the Heresy should be very much aware of.
The worlds chaos control in the Eye of Terror are, compared to the Imperium massively limited. Every planet destroyed is one less the Imperium has, but the Imperium has a lot of planets, and to get close enough to Exterminatus one you need to get past a defensive fleet and the planets defences. You'll be expending ships everytime.
The end result is just putting some pace between your supplying worlds and the Imperial front line planets.
Plus of course, Chaos supplying planets are suffering the weird time dilation of the Eye of Terror. For every year of production by the by worlds in the Eye of Terror Imperial worlds might have 10 years or more.
So even with a planet destoying weapon you have to guess they were still aiming to target only specific planets for destruction while taking others.
Which brings me to my bugbear. What's the one time you, as clear thinking Chaos commander (if one can said to exist). Why would you drop on to a frozen Death world, with zero production capability that houses a legion strength chapter of Space marines. DAMNIT AHRIMAN YOU'RE SUPPOSED TO BE SMART! Why didn't you destoy Fenris rather than going in for a close quarters rematch?