They apply to all flights. Thirteen hours, six hours, three hours, one hour, stuck in a metal tube with recycled air, you smell like an ashtray when you get off and people smoked. Unless your filters are exceptionally efficient (which would be a surprise, they certainly weren't back then), the length of time is irrelevant.
Besides, why would anyone need to light up on a one hour flight? Or a two hour one? I welcome things like an airside smokers' lounge (as someone else pointed out, like EMA now has) that allow smokers to get their fix in while they wait, but that's as far as you can go.
I probably sound terribly militant, but I'm not. I just feel it's unfair on the majority to have a minority impose their will because they chose to start a habit that is now addictive.
S.