I don’t think the fonts are that small… Maybe its something with your system? Installed fonts, resolution, etc?
plus, you can read little roman characters right? So why wouldn’t someone be able to read their native characters real little?
I also think it might be to do with fonts. I find that most Japanese websites are legible, but very notably Wikipedia is real bad, especially vertical strokes are often near invisible. I think this might be to do with a standard font size on Wikipedia as well, which isn’t awfully suited to Japanese, which has a very variable information density.
A second point as well is that, presumably, native Japanese people when reading don’t examine the character in its entirety, just enough to determine it from others that might also appear in the context. You know how in English if you garble the middle of the words in a complete sentence, the sentence itself will still remain legible.
I presume the same way we read English…increase the font size and zoom in. Also they start children off with giant fonts (in english) and progressively move you to smaller fonts…until our vision fails you and then you move back to larger fonts.
Aka the more you read, the better you will get at reading smaller fonts…until you can see anymore.
I would guess that fluency makes it a non-issue. Many characters would be obviously distinguishable and I would expect the context they are in (both words and sentences) to take care of the rest. But again, that’s just my assumption.