If it was the motherboard that died, and the hard drive is undamaged, then all your photos are fine.

You're not seeing them in the Pictures directory because they are stored inside iPhoto's Photo Library, which is a package.

All you have to do to "recover" them is to launch iPhoto *holding the option key down.* It will ask you if you want to open (or create) a library, point it to the one on your now-external HD and you should be right back where you were.