Calories In vs. Calories out - at least at the level that any reasonable person can measure it - is worthless. I that it's easy to remember and even sounds kind of cool - but science doesn't support it. There are plenty of studies that show things eating the same number of calories and having dramatically different weight gain or loss.
Measuring what you eat and estimating how much you burn by your daily activities is clearly not enough to accurately determine if a person will gain or lose weight.
Here's two studies - you can find many, many, many more....
Here's a study where different groups of mice ate the same number of calories, but at different times of the day/night, and the different groups saw different levels of weight gain/loss.
Here's a study where different groups of mice ate the same number of calories, but one group had a low-gi diet and another group had a high-gi diet. The high-GI diet mice gained more weight than the low-GI diet mice.
I'm not trying to be argumentative, and I like the 'gist' of the Hacker Diet. But the entire premise of the diet doesn't hold up. Not in any way that a regular person can measure. Maybe, the habits like how much you sleep or when you eat or the GI index affect either how much you burn (even though your activities are no different) or how effective your digestion is - but until you've got a magic toilet that tells you how many calories you've just dumped off and a watch that will tell you exactly how many calories you are burning - it's not useful.
But yeah, the general idea of eating less, eating better, and exercising are all generally good things. Those things are hardly unique to the 'Hacker Diet' though. I don't know of anyone who eats healthy food, in moderation, and follows some sort of physical fitness routine who isn't in decent shape; but grossly oversimplifying what's going on doesn't benefit anyone.