Probably, yes. Thanks to the massive beaurocracy that the Imperium's tied up in, it's quite likely there are dozens, perhaps even hundreds, of independent worlds which quietly go rogue without anyone noticing. Though eventually, the Administratum will realise that they're not getting their tithes from some forgotten backwater, and the Imperium will take steps to retake their world.
One problem, though, is these independant worlds are very vulnerable. They often don't have the capability to detect and remove psykers from the populace, so there's an increased risk of possession or daemonic incursion. They can't call for help, so if they get invaded, they're probably stuffed. And there probably won't be as stringent measures in place for weeding out heresy, so there's a good chance chaos cults might start cropping up.