Hi!
I wouldn’t do this. Simply not meant for thermal paste and it can give you some issues.
But you can use special thermal paste that is meant to replace thermal pads! Like the K5-Pro.
The most easy way is just to replace the thermal pads for new ones. The most PS2 consoles do run fine these days without overheating or whatsoever.
I would first check how it goes, if it’s making a lot of noize, or experience overheating, I would replace it yes.