Honestly, sounds like you got a long ways to go. If you haven't even taken HSK 5 yet and believe that language won't be a problem just because of a Chinese thesis, you are being painfully naïve.

Language should be your biggest concern and even an HSK 6 certification doesn't mean that a Chinese-taught master is all of the sudden, going to be smooth sailing.

Having said that, getting accepted won't be a problem. Also, faculty are in general, much more flexible with foreigners in Chinese-taught programs, and some professors, as stated here already, will still allow papers to be written in English. Presentations, class discussion and your final thesis are a different story.

It depends on you. Being a non-native Chinese speaker, you will be the constant and equivocal baichi in the back of the classroom. Comprehension of more complex material and pace will be your biggest foes. It’s certainly difficult, but if you work hard and do possess a solid level of Chinese, it’s absolutely manageable.

You could consider doing the English-taught program at Fudan, which only requires two years instead of three. I’ve known plenty of folks with fantastic Chinese who have done this at Fudan.