As long as you are quiet and stay out of the way there usually is no problem with it. Its best not to go up there during evolutions like entering/leaving harbour or a RAS.
But I am basement dweller and I go up all the time in heavy weather. I just be quiet and stay out of the way. Anecdotal point, as a non-smoker now I would go days and days without going outside and seeing sunlight on my last deployment. The med in the summer is glass clam.
@Navy_Pete maybe its because we are tied at the hip but I have never needed permission to go into the MCR. Its not a place I hang out, but I will go in to chat with someone I need too or make a pipe. I defiantly feel welcome.