A quick google search will confirm he did, as well as staying at a former backpackers' hostel across the soi (now the 7-11), although he lived longer term at Kanit House 504.
Remember, Soi Nam Duplee was a backpacker hangout, back in the day. The TV series "The Serpent" took some dramatic liberties for the sake of the story.
From an online Book Review: I have recently been on a Bangkok binge, having read Bangkok Burning (by Robin Newbold!), Lawrence Osborne's The Glass Kingdom and now the trilogy with the The Serpent. Having stayed at the Malaysia Hotel, where the protagonist - Charles Sobhraj - picked up some of his victims, and knowing the city extremely well made this true crime book a particularly poignant, if salutary tale.