Five-inchers start to get a little heavy. People with small hands can have difficulty with them.
But, the big reason that they're somewhat uncommon is doubtlessly legal. A five-inch blade really starts to look menacing and it's very hard to justify it for day-to-day use.
Furthermore, I disagree that a long blade is necessary for self-defense. Most of the major arteries are within an inch of the surface of the skin. Yes, a longer blade does give you a bit more reach, but unless you go to a very long blade, eight inches or more, that advantage just isn't very large. Between a three-and-a-half inch blade and a five-inch blade, you get one-and-a-half inches of greater reach, about the length of the first segment of your thumb. That's just not much difference. Furthermore, a smaller knife is usually a faster knife. That advantage can make up for the length.
It's a little bit like the arguments that rage about gun caliber for self-defense. I've heard people say, "If you ain't packin' at least a .45, then you ain't packin'!" And that's true in a way. Most people find a full-size .45 to be to large and heavy to pack most of the time. So, they leave it at home most of the time. In other words, they ain't packin'.
In 1995, the last year that I heard any data for, about half of the lawful civilian self-defense shootings in America were done with .15, .22, .25, or .32 caliber pistols. Why? Simple: these smaller pistols are what people can comfortably carry. So, these smaller pistols are what people do carry. So, these smaller pistols are what people have when the need comes up.
When @#$% does happen, the caliber of gun that you left back home in your safe doesn't matter.
If you've never experienced one, a 5" S.S. or brass balisong is one big, heavy chunk of metal to carry around. Like that full-size .45, it's the sort of thing you'll probably be tempted to leave at home most of the time.
But, a 3.5" with skeletonized Ti handles (did somebody say Tachyon?) is a comfortable knife to carry with you all day, every day.
When @#$% does happen, the length of the knife you left back home in your safe doesn't matter either.
As the old saying goes, "It's not the length of your blade that matters, it's how you wiggle it

"