I restored an IHC model 80 snow blower. The pto had been converted to 1000 rpm. I left it like that and the gearbox has had no issues.
Friends of mine in Manitoba have a Universal tractor. I don't know the model but there is a provision in the transmission to run the 540 pto at 1000 rpm. They regularly run their 540 rpm snow blower at 1000 rpm. Again no problems other than the snow blower now throws snow quite a bit further.
There is much wisdom on this forum saying that the gearboxes are designed to run at 540 rpm and that they should stay there. Then there are those who run their gearboxes at 1000 rpm and realize that even though the gearboxes are designed to run at 540 they actually perform quite well at 1000 rpm. The objective is to move snow further away and this easy modification does that quite nicely.
I am not an engineer but I do know that if you double the speed of a shaft you can transmit 4 times the horse power through that same shaft. That's why as tractor horse power increased in the early 60's, 1000 rpm pto's came into existence. I'm thinking then, that it's probably easier on a gearbox to run it at 1000 rpm rather than 540, all else being equal. The only question that comes to mind is oil sheer destroying lubrication because of the faster speeds involved. Again that's probably not an issue as there are many gear boxes that turn faster than 1000 rpm.