As said cable length is a problem but I have managed to do just what you are thinking of doing and a bit more. I've made my own custom cable 2.5" female -> 3.5" female -> 3.5" male (aprox 15-20cm) that goes to my internal HD and then to the back of my Amiga case as an external port and from there I have have a short (aprox 35cm) cable to an external backup HD. So it is possible but try to minimize the cable length or you will run into all sorts of trouble.
I hade my harware hacked A1200 on display at the AmiGBG03 fair and you can see some of the mods incl. the IDE port
here.
