We don't have enough information to be sure whether it's really more difficult to Apparate in the dark.
The case for yes
From Apparition lessons:
“Step one: Fix your mind firmly upon the desired destination,” said Twycross. “In this case, the interior of your hoop. Kindly concentrate upon that destination now.”
“Step two,” said Twycross, “focus your determination to occupy the visualized space! Let your yearning to enter it flood from your mind to every particle of your body!”
-- HP and the Half-Blood Prince
The Apparating wizard must "concentrate upon" their destination, but it's not made clear exactly how this concentration works - maybe visualisation of the spot is required, in which case it would make sense for it to be more difficult in the dark.
More importantly, what does the wizard have to do when they land? There must be some last-minute adjustment involved (possibly subconsciously), to take account of factors such as uneven ground or the exact altitude of the destination spot. I don't think there are any canon examples of Apparating into mid-air, but it would certainly be quite a feat to be able to concentrate on one's destination well enough to be able to fix one's height aboe the ground so exactly that one's feet land without a bump. Since no such bump is described, perhaps the Apparating wizard takes a glance at their surroundings while they're in the process of materialising and adjusts themselves slightly so as to land more smoothly. All this would probably be subconscious.
Another excellent point - thanks to @JanusBahsJacquet - is that the point of Fred and George's departure (their own bedroom) as well as arrival (Harry and Ron's bedroom) was presumably also dark. The twirling motion on the spot that's used in Apparition would be harder to do successfully in the dark and might cause them to be imbalanced as they're Apparating - hence the imprecision in precisely where they land.
The case for no
Fred and George are the ultimate pranksters. Apparating on top of their younger brother's knees is just the sort of thing they'd do for a laugh, and then they could shrug off his indignance by coming up with some excuse. He was only fifteen at the time, and would believe whatever nonsense they told him about Apparition in the same way he half-believed their stories about wrestling a troll during the Sorting Ceremony when he was eleven.
And JKR probably didn't plan out all the details of Apparition. It certainly seems to work in all sorts of circumstances - Apparating to a place one's never been before, for instance - so the answer to "how do you manage to land perfectly with your feet on the ground?" could be just "because magic *waves hand* ". Being able to visualise your destination perfectly can't be a requirement if it's somewhere you've never been, so why should it matter whether or not you can see your way around when you arrive there?