I have a 60 GB and it's not noticeably loud. I don't have experience with the 40 or 80 GB models so I can't compare, however.
I would say it's worth going for the 80 Gb over the 40; personally I never had a PS2, and it's been really nice to be able to play them on the PS3.
The card reader is also a useful thing to have just for future ease of data transfer. Nonetheless, there are USB ports so you could always just use a USB card reader with the 40gb version.