So how bad is the Nirnroot glow in your playthrough? Seeing as you have clocked in 400 hours can you notice such a big difference?
If you notice my above post, I do my best to pick nirnroots along the way (as well as pick up stray arrows and cleanup enemy weapons), but they still manage to stack on me sometimes. Once in awhile I still discover one I was unaware of in an area; and most of these, ironically, I find simply because their glow stack has gotten so large.
Since Whiterun is my character's home, that city is my hub and the area I spend the most time in. Precisely because I travel there a lot, I don't hunt nirnroots every trip there; if I did, the game would've become a chore instead of fun a long time ago. I go on a nirnroot expedition every third or fourth trip there, usually during the evening or nightime, and use the glowstacks to help me quickly find them.
For me, it's about finding the balance between the game being a chore vs. enjoyable. As it is, I've already diverted from how I'd like to play the game quite a bit so, e.g., I'm not OCD enough to make a map of all the nirnroot locations and run around Skyrim picking them constantly. As I stated before, I don't know what the threshold is where the extra glows begin to slug down the game to the point of freezes/crashes, whether it's more an additive between numerous glowstacks in an area and/or whether a single, *super* stack is enough to burn that bridge.
I'm approaching 500 hrs. on my playthru and my save file is 12mb. "Knock on wood", so far my freeze and crash issues have been minimal. Otoh, I wonder how many of those hours were spent cleaning up the world vs. just playing the way I'd like?
Edit: And keep in mind that there's sort of two seperate issues involving the stacks. The first is that each glow in a stack acts like a persistent object and, therefore, has to be included in the save file. Thus, every glow for every nirnroot is being loaded/saved everytime you load/save. Second is the visual, graphical hit to the system as it has to calculate how to layer those stacks and present them when it's actually necessary to draw the nirnroot.