In general, university admission in Germany is pretty bureaucratic. You have to fulfill general requirements, and if you meet them, you get into the program. The requirements for a master's degree are a bachelor's degree in the same / closely related field and proof of a high school diploma (in Germany, Abitur). For foreigners, proof of language proficiency is often required as well. Letters to the admission office explaining why your grades are not as good as they could have been will probably not be read and will certainly not matter.
For a reason stated above (general requirements), the university asks for a high school diploma---not necessarily because of the grades but to see that you finished high school. Many master's programs will admit (almost) anybody that fulfills the abovementioned requirements, as applicants do not overrun them. Others are more competitive, but the deciding factor will then either be the grade of the Bachelor's degree or a combination of BA grade and high school grade.
Ask the uni(s) you want to apply to about admission requirements; with a good BA, you will probably quickly fulfill them.