For most of the story, Martin seems like an amiable and hard-working man and is not considered a suspect because he was on the other side of the bridge when Harriet disappeared. Of course, that's because although Harriet's disappearance is linked to Martin, he actually had nothing to do with it and is as puzzled by it as everyone else.
Martin didn't kill Harriet, but he does kill many other women. As a teen he witnesses his father's rapes/murders, and participates in at least the rape/murder of Sarah Witt. One of his victims, Lena Andersson, was his school classmate, the year that Harriet disappears. There's no explicit confirmation on whether he was killing between 1966, the year Harriet disappears, and 1979, the approximate year he builds his house on Hedeby Island, though for such a long time span, it's certainly plausible that he was.
From Salander's perusal of his "death book," it's revealed that from the time he built his house in the late 1970s he kidnaps dozens of women, tortures them in his basement, and then kills them. After he's done with the women, he dumps their bodies at sea with his speed boat. Like his father before him, he has all the money and power he needs to commit these crimes without being noticed, though Martin proves himself as more cunning than his father was; he chooses the most vulnerable women – prostitutes, immigrant women, women with drug problems, and he chooses women whose families, if they have families, won't notice they're gone, or won't have the means to pursue a major investigation.
"[…] I'm more of a serial rapist than a serial murderer. […] most of all, I'm a serial kidnapper. The killing is a natural consequence – so to speak – because I have to hide my crime."