Do students from countries that teach native languages considered to be quite difficult (e.g. Japanese) generally take longer to master that language? Or does the power of being surrounded by a particular language at home and in society overcome the difficulty of said language? Are there simply too many factors that influence how well one student learns their native language compared to others?
It depends on what you consider 'mastering' the language to mean.
Firstly, I would have to say that the 'difficulty' of every other language is relative to the language you already know, and perhaps, that answers your question in itself, but I'll continue.
If you consider just the speaking, for example, no language is more or less difficult than any other language for a speaker who is starting from no base language. The verbal language is just a means to express you needs and wants. It is basically just copying what you hear and then repeating it because you have realised that this pattern of sounds, whatever pattern it actually is, is going to get someone to give you something you want or do something for you.
Naturally, the written aspect of the language can differ in the length of time needed to learn it: learning the Kanji in Japanese is going to take much longer than learning the Latin alphabet. That being said, the Kanji could be considered an equivalent to words in English, and there aren't many people (if any) that can say they recognise and understand the meaning of every single word of the English language, or any other language for that matter. Another thing to mention would be that some of the words are rarely used and often forgotten even by the first language speaker (I've seen this with my father who has forgotten how to write a lot of the Chinese characters through lack of use—he can still spell and pronounce them, but sometimes he doesn't even recognise them—and he is typing to his brothers and cousins on Facebook or Line every day!).
It doesn't slow down early education, though, since the language is taught parallel to other things like Maths, and other subjects. The actual teaching is started a bit earlier (for the Chinese, at least, since they are taught the phonics before they learn the Hanzi), so there is already a lot of understanding of the language even without the 'official' writing systems.
Now, going back to your question about 'mastering' the difficult first language, this depends on whether you consider this to have the amount of knowledge of the language that is equivalent to an average person in any other language, ie. an ability to hold conversation and have a deeper understanding in a few areas, or a person who has studied the language itself deeply. Most people never get to the point of 'mastering' their first language, no matter how easy their language is said to be.