According to Eighth Doctor Adventures, the Dalek Supreme found out what would happen to Skaro, so it had a nearby planet terriformed to look like it to fool the Doctor into destroying it, thus leaving it alone.
- And even if the novel is not considered as canon, the Doctor is a time traveller. No further explanation is necessary, really. (additional: Actually, the prequel seen only in the US on iTunes reveals the Doctor himself didn't travel to Skaro, but was transported there. Still, he could have been transported through time to a point before the planet was supposedly detroyed.)
- When Skaro was supposedly detroyed in "Remembrance of the Daleks", the dialogue implies that its destruction also involved time travel, so we don't know when that destruction was meant to have occurred.