Hori pads definitely feel good to hold and play with for general use, but I don't think the price is worth cutting up for a portable. If you're into playing n64 games the old fashioned way (not in portable form), get one, and then seriously consider whether or not it is worth cutting. I still think the gamecube joystick is way better than the hori pad (someone who owns both, let me know if I'm wrong haha).
Funny story, I actually own 2 hori pads, and the whole reason I got them was so I wouldn't hack them open for a portable... because no other controller would survive while I was around experimenting... but I knew that if I got an expensive controller I wouldn't hack it open and I'd always have a controller around for general use. I have a transparent smoke n64 console for the same reason
edit:
DARNNIT! You said right in your post that that's what you were planning on doing, just using the hori for general use and not for a portable. I'm an idiot lol.