Lot of my chara has died or floated to the surface. Doesn't seem to affect the fish, but it is unsightly and might be clogging my diffuser heads. Should I worry about it causing a fish kill? Should I remove it or is it fine?

I'm pretty new to pond maintenance and my pond is showing good signs of high nutrient levels. It's in its first year after de-mucking. I have not had any real issues with FA or Chara although both exist in the pond. If I had masses of floating slime I would remove it to help reduce the nutrient levels which would also, reduce the amount of muck accumulation, improve aesthetics, and reduce the risk of a DO crash. With that said, there are ba-gillions of unmaintained ponds out there that do just fine with excessive floaties. It sounds like you have a pond to be proud of, I'd rake it out if you can bear the time and effort. I can't think of a reason not to.