Winter tyres or winter wheels?
I'm assuming you have rim brakes, since you are asking about wear and aligning brakes.


Winter riding will wear out everything faster. The rims are going to be wet and dirty for most of the time, and the same goes for transmission. It might be a good idea to use any old equipment you don't care about as winter parts. The exception is that better hubs have better sealing. 5000 km isn't that much for rims, by the way.
Unless the rims are exact same width (or the rotor is aligned exactly the same) you'll have to adjust brakes every time you switch wheels. Possibly the derailleur too.
New cassette on worn chain will be noisy, wear out the cassette fast and skip if the chain is worn badly enough.