It's a hardware thing, so you can either take the fan off its original circuit and power it with your own circuit... or just use a quieter fan.
Originally Posted by pelago
I don't think that it's wise to disable that behaviour though. While you are right to say that the laptop HDDs (SSDs don't even have moving parts, so they probably won't be affected) don't produce as much heat, it's probably a good idea to ensure that the air circulation stays good or it'll not be too healthy for it.
Just FYI, the SCPH-39000 series has the loudest fans amongst all PlayStation 2 consoles. My SCPH-10000 is so much quieter. >_>
SCPH-10000 S. MINOKAMO v1.01 (Defunct)
SCPH-10000 S. KISARAZU v1.00 (faulty)
SCPH-15000 S. KOHDA (With warranty seal!) :D
DESR-5100 S. EMCS