My internship is going to sponsor my bachelor's thesis (which will require more hours in the office). Should I ask for more money?
I don't think you have a lot of leverage here other than by disadvantaging yourself. 

First, scholarship money is not always abundant and people like to spread it around to help more people, rather than to concentrate it. 

And, you are getting something for your work, beyond the money. You are getting a degree. It isn't that they get your work for free. You made an agreement, I think, if I have a accurate reading here. Live up to it. 

I think your statement that the company is holding you hostage is misplaced. In fact, they are helping enabling your future. Even just providing a project that you can develop into a thesis should be worth something to you. 

I suspect that starting over with a different situation would be worse for you in every way: time, money, and more.