Seems like your perspective on your Japanese journey is in need of some pondering, if I may.
Why are you learning Japanese? To read and enjoy Japanese medias I assume, right? If you are already reading and enjoying yourself, then all that's left is to continue. Encountering words you don't know isn't something that should bug you, it's normal, and that's how you learn. What good would it do to anki all the Japanese words ever? To then being able to read without having to stop? I think you know very well that's a bad idea, as your brain will likely remember words much more easily through encountering them while reading rather than in zombie-anki mode.
Japanese doesn't share roots with European languages, that's why vocab is a hurdle, as opposed to learn English from French, or Italian, German or Spanish and vice versa. To learn Japanese you need put a little more efforts because of Kanji and such, so I can understand why it can feel frustrating at times, but ultimately... there's just one thing to do : continue reading.
That's just how I personally see it, as someone who still considers himself intermediate.