Oh, I think it's pretty clear (at least from my reading of the show) that Sarah lived on the TARDIS. Certainly not when she was Three's assistant, or during the events of "Robot," and I'm sure she still had a place to go back to as of "Terror of the Zygons," but after that, they were only on earth one more time in her time, and only interacted with UNIT one more time ("Android Invasion").

I've always assumed that, between the Zygons and "Hand of Fear" that someone at UNIT (Harry or the Brig or a combination) was making sure that there was some kind of cover for her absence, and I think she rang up her editor in "Seeds of Doom" to keep up appearances...but I always assumed she was off-planet for an earth-time period of 9 months to 2 years.