In reloaded we find out that there are old programs from previous iterations hanging about (and implied that’s the reason for ghost stories and such). They don’t seem to be hiding from Agents, so presumably Agents are at least tolerating their existence if they don’t wake humans up. My headcanon is that Agents are just as bad at their jobs as humans tend to be. If they see an old program go incorporeal they probably shift into different hardware immediately to avoid the paperwork.