The Nightmare Scenario
Hear me out. We all know the logic behind email spam: the cost of sending out a million messages differs little from the cost of sending out a single message; even with a minuscule response rate, sending enough messages can mean a visible return on investment; spam "offense" always eventually overwhelms anti-spam "defense."
The same logic could apply to molecular manufacturing spam, but MM-spam could take myriad new forms. Advertising messages etched into whatever objects get made by a nanofac. Code that tells the nanofac to use all available nanotoner to continuously print out small, mobile commercial-shouting bots. Hacks that instruct a nanofac to embed into the hardware of any new nanofac it makes commands to add commercials on whatever the new nanofac makes. I'm sure I'm only scratching the surface here, and that far more insidious and hard-to-root-out forms of nanospam are on the horizon.
It seems that every digital technology capable of displaying a message and hooked to a network eventually becomes the target of spam. It's highly likely that nanofactories will be online, along with everything else in one's house or community, for reasons of hardware updates and design transfers; those here old enough to remember floppy disks know that malware can travel via sneakernet & disk quite easily, too, so being unplugged is not the same as being offline.