I use a flail in the woods a lot, I have vines and branches come down or shoot up and hit the shaft.
With the guards, not a big issue, though I do try to cleanup anything like that before I do a run. But in brush and tall grass, anything can happen and bind up.
Outside of the woods, probably would not be an issue for me, but they are on and staying there.
Mine are not quite so big though as that picture, so they don't really bother me. I have a shield on the stub and on the flail side which covers my needs. So the end shaft guards are extra, the sleeve that guards the shaft works great, I've seem vines hit it and nothing happens, too slippery.
I agree, weigh the risk, like with any tool though, but then again I never run the PTO out of the seat and all my safety switches are working.
The IH I was on as a kid, had no safety anything, but it was used mostly to pull plows and wagons.
I don't remember using the PTO, but our neighbor did all the field haying, not us. I don't miss a clutch when I use my current tractor, but I don't have large fields, lots of small ones and woods.