I suspect the issue that Mercedes is concerned about is rubber weatherstripping being frozen and tearing if the roof is operated in extreme cold. I doubt that it is hydraulic seal related. I've been out on the freeway at 0c with the top down many times. With respect to the roof, my research showed that Mercedes rated it to a duty cycle of 800,000 actuations, if memory serves. I use it all the time. Often several times a day. My feeling is that it's much better to use it because it keeps the seals lubricated. Mind you, I've also been on the freeway in pissing down rain storms with the top down. It always amazes me how little water actually gets in the car in situations like that.
I mentioned it before, but I feel that the roof is similar to the front seal on an AC compressor. The front seal doesn't really seal the system and keep the refrigerant from leaking, it's the oil on the seal that keeps it from leaking. As such, if you shut your AC off for a protracted period it's not uncommon for the refrigerant to leak out. Where you often see this is in heavy-duty equipment (like excavators etc) that sit over the winter. The oil drips off the seal and refrigerant slowly escapes.
This is one reason the manufacturers turn the AC on in the defrost setting. It's better to defrost a window using dehumidified air (AC on) but it has the side benefit of running the AC in the colder months and keeping the seal lubricated.
In my mind, the roof circuit, viewed as a whole, comes down to 2 things, the brushes in the hydraulic pump motor (if it has brushes) and keeping the hydraulic seals lubricated. If the 800,000 duty cycle is to be believed, and I have no reason to doubt it, my guess is that would be the only two things of concern. Just my .02c
As for storing the car, I'd have the roof and windows up, but that too would depend on location. A friend has a mint low mileage 3rd gen SLK. Just a beautiful car. He had no room at home for it over the winter so he put it at someone's place (sounded like a barn). Rats got in there and ate the wires. Apparently they had to pull the engine and transmission to repair the damage because they had to make a custom harness. He was told there were real problems getting a new harness from Mercedes... due to the issues in the Ukraine...
GM, Ford and Chrysler have used plastic loom on their wiring harnesses for years...ahem...cough...cough....