I have a thing about getting every unpotted Crimson Nirnroot but the one at the top of the waterfall. I tend to get 39 every time, but I also play Skyrim alot.
Blackreach will respawn after 10 days, so if you don't visit the location during that period of time, the nirnroots should also respawn.
I turn up the sound effects and turn down the music. It makes the nirnroot noise a bit more noticeable from farther away. It's still tedious, but not quite as much.