I don’t want to be a bother. I don’t want to be a bother to you. I don’t want to put you out.

To me, both of those options are similar. But yes, both of those have a similar meaning to 'be a hassle'. Although perhaps it is more 'bother/trouble you more than necessary', since by asking the question, you have already bothered/troubled the person somewhat. I don't want to bother you too much.