Generally on OEM computers, you are stuck not being able to adjust the fan speed. Some newer oem's have their systems setup to vary the fan speed on demand. Since your sons computer is an Athlon XP and is older, you can't adjust the speed unless you add an aftermarket hsf and a fan controler (some come with it). Anthlon XP's, especially the Barton core's ran pretty hot, which would explain the high rpms for his fan.
To answer your other question, yes fans will get noiser the faster they go. Especially the stock coolers, since the fans are usually smaller and lower quality than aftermarket hsf combos. Larger fans will move more air at a lower spped, meaning less noise. You sons computer is probabl yjust fine using the current setup since the noise isn't bothering him.