If you think the hub runs cooler with a smaller fuse you are just imagining it. The only effect of using a fuse smaller than called for by the device's specs would be the fuse blowing unnecessarily. Also, a fuse doesn't protect from power spikes. It takes a good surge protector for that.
I think what he meant was, the fuse itself was getting hot. There have been reports of the plastic body of the stock 40A fuse melting and roasting things around the board.
https://bitcointalk.org/index.php?topic=336911.0Hope everything is getting better for you, SSB.
Thanks for the clarification. In that case my guess is a batch of defective or mis-labeled fuses since all things being equal a lower rated fuse should have higher resistance and would be the one to run hotter since, after all, the way they work is under excessive current they get hot enough to melt and a lower rated fuse would melt at a lower current (amps).