Nanomachines were minor, as noted, before the Shutdown, after which they were the bleeding edge.
When 4th rolled around, with a more transhuman bent than previous editions had, nanomachines got pushed to the forefront, drawing from the cyberpunk of the day, which always had a nano-focus. The main problem was that, like RFID tags, the tech wasn't quite understood and quickly spiraled out of hand. With any nanotech story, if you don't have solid rules in place, the "Grey Goo" issue stumbles out like a drunken uncle, shouting obscenities while waving a beer around, demanding that you take time out of your day to deal with it.
So, the bridge from 4th to 5th saw a lot of work being laid down to not remove Nanofunctionality from the world but to pull it back from where it was, which was far too big a deal. the CFD storyline saw nanomachines blow up into a big problem again, dominating the spotlight and demanding to be dealt with, showcasing, once again, that when you let the genie out of the Tequila bottle, well, you have a whole lot of things to deal with.
Right now, things are pulled back again. Tamed? I wouldn't say tamed, but not madly rumbling around again. We'll see what the future will bring. There are certain lot elements that can easily slip away and be massive problems if you don't ride herd over them. For instance, if you have a giant sea of data and processing power like the matrix, and you have AIs, who are purely code, who can write computer code, what's to stop a single AI from making billions of copies of itself and infesting every single computer on the planet? At an ever-increasing speed no less as each copy created can start creating copies of itself as well, turning exponential.
(Similarly, if you have an infectious race, like vampires or ghouls, they can *explode* across a population in a shockingly brief time. The problem's not restricted to technology so don't take this as some kinda of anti-nano screed!)
Always important to keep these things under control and tell the story you want with the tools presented. The transhuman stories are better left to Eclipse Phase, for instance, while Shadowrun focuses on other things. This means thatnanites are on the back burner until needed. Will they be a big story again? Maybe. But you gotta be CAREFUL so that it doesn't turn into another drunk uncle.