Hi,
I've had my IS 250C since 2010 and it's still a great car 5 years on. No problems with the roof beyond the odd squeak and knocking sounds, but it is a lot of metal to hold in place.
There is an obvious price difference from the standard saloon, mainly due to the convertable roof and stiffend body. The spec's are almost identical per model. There is more weight in the 250C as you'd expect, but you also wouldn't notice unless you are a serious petrol head (and I doubt you'd be getting an IS250C if you were).
I use mine as an everyday car, and always look forward to the days the roof can come down. The one thing you will notice, you don't see many on the road, so there is an element of feeling exclusive still.
Good luck in your search. I'm now wondering if it's time to look at the new RC F ??!! Would like a convertable though :-)