Soyuz can dock to deserted stations, or at least could in the past. They had to do it all the time with the Salyut stations, and I suspect it is how the first docking with the ISS went down as well.
Technically there is berthing and there is docking. Berthing requires that both sides cooperate, but docking doesn't necessarily require this. However while docking both sides are very nearly always under control (with the deserted side under robotic control).
Non-cooperative docking has only been done exactly once in the history of human spaceflight on the Soyuz T-13 mission to the Salyut 7 space station [0]. In addition, Wikipedia mentions a few unmanned tests.
In practice, all spacecraft docking and berthing operations are fully automated and no human intervention is required apart from emergency conditions (which have never occured). The last intentional attempt (1997) at manual docking ended up in a bad collision between the Mir space station and a Progress spacecraft [1]. The last Mir mission (Soyuz TM-30) did the last few meters under manual control. ISS crews are trained for manual docking but I don't think has ever been necessary.
In the hypothetical situation that the ISS would be left unmanned, it's extremely unlikely that they would decide to (or have time to) power down the attitude control systems (control moment gyroscopes and thrusters). So even if the station ended up unmanned, it's not likely that it would be non-cooperative (ie. out of control). If all the attitude control systems would disabled because of damage (e.g. fire), the station would probably not be salvageable.
So it's possible but very unlikely to have a scenario where a manned mission would need to manually dock an out of control space station. But it has happened once before, so it's not impossible either.
Technically there is berthing and there is docking. Berthing requires that both sides cooperate, but docking doesn't necessarily require this. However while docking both sides are very nearly always under control (with the deserted side under robotic control).