I don't believe there is any basic difference in meaning, but there would be an implied difference based on emphasis. "I think this is not beautiful" is a much stronger opinion than "I don't think this is beautiful". At that point someone might just slide straight into the meaning of "omg this is horrendous-looking"

What's your take on it?

There's not really a "difference" in meaning, but the latter is much more common and just sounds better. The former is something that non-native speakers are more likely to say.

So what are you trying to suggest?

I consider she is not beautiful. I suppose she is not beautiful.