When I type something on my computer it can be easily filed forever into a giant hierarchy of files and notes. When I write something on an index card it gets in my way until I deal with it.

That sounds like a disadvantage of index cards and it is — but only if you have the wrong goal. My goal is not to find the easiest possible way to write things and file them. The the goal is to remember what I’m writing so that I can use it later. This is why I stick with index cards, notebooks, and Post-It notes. Their pain-in-the-assness is their greatest benefit.