They seem to just be relocating to other parts of the city as formerly homeless-heavy areas like parts of SOMA and the mission "gentrify." I walk through the loin twice a day on my way to my office on market st near the post-apocalyptic parts of SOMA and see a higher concentration of homeless in those areas than I used to. Perhaps you're revisiting the parts they've left or my un-scientific observations are wrong.
They also seasonally relocate, heading south in the winter and spreading out in the summer. Seattle's transient homeless population is largely gone by mid-December