First, I don't have a lot of experience in inflatables. Audrey Sutherland, a world class kayaker and sportsman, uses them exclusively and has written pretty extensively about them, however. Her opinions are a bit hyperbolic, but she is really an inflatable advocate. That she also advocates, in rough conditions, that she get into the boat and be tossed into the ocean by her fellow paddlers to exit the surf zone suggests to me that there are some issues she just glosses over.
As with all boats, however, it comes down to design. Many inflatables are high sided and, as a class, tend to be more windblown than other kayaks. Others, I hear, don't have this problem. There are more limited hull designs possible with inflatables, however, and I would be skittish taking them in areas where punctures are a possibility (rock gardens, surf/moving water +underwater obstructions).
Sorry I don't have more to offer on the subject.