At a recent panel to promote Louie for Emmy consideration, C.K. explained why. Although the panel wasn't captured on video, a writer for Hitfix recalled C.K.'s story (and a lot of other great stuff about the show) like this:
"How did C.K. wind up doing only 8 episodes this season? Well, originally, he wanted to delay season 5 so he could film it in the fall, since shooting previous seasons in winter — particularly the recent crippling New York winters — was wearing him down. Then, the night before FX chief John Landgraf was going to announce the delay, C.K. smoked a lot of marijuana, felt a burst of inspiration for stories he wanted to tell this season, and wrote pages and pages on his computer, breaking out all of what he felt would be an amazing season. He called Landgraf and asked if he could produce on the original schedule; a frustrated Landgraf told him they had already allocated most of his budget to other shows, and the best they could do was a half-season. So C.K. agreed, Landgraf announced that, and in the sober light of day, C.K. finally read what he had written... and it was gibberish. He didn't use a single idea or joke from it in making season 5. Don't do drugs, kids. Or, at least, don't make big decisions while high."
C.K. has said before that he doesn't smoke weed often, but when he does, it's usually a little too strong for him.