IMO, you should start looking for someplace to back up all your data to and then replace the HD.
HD's are not supposed to make "noises" other than the normal sounds of the heads positioning themselves on the platters. It may have something to do with heat, or lack thereof. After sitting all night, the initial start seems to be giving it trouble but once it has come up to speed, and is warmed up, the problem no longer exists.
My advice, back up ALL you data to an external drive and replace the HD with another, larger one.
Now would also be a good time to update the OS to 10.4(Tiger) or at least 10.3(Panther)
I am using an iMac G4 3.3 .OS 10.2.8. I use Cox.Net for my for my internet connection and airport. Often when I first start up my disk sounds like it is stuck and i hear a sound like when there is a scratch on a CD. After a few tries my computer starts up. After this initial start up I can shut down and startup without any trouble except when I shut down overnight.