I've had two desktop A3000s running CybergraphX on a GVP Spectrun 24 board. The stock 25MHz '030 definitely got a noticeable speed boost in rendering screen redraws and pulling up JPEG images with the A3640 installed. It was even more noticeable after you get used to it and then yank out the board. I had no overheating issues, but the original heatsink will be too big to fit under the floppy drive bays. You'll either need to cut a hole in the sheet metal, or find a lower profile heatsink. I was lucky enough at the time to find a low profile heatsink that fit and extended off to the sides to allow for more surface area cooling.
I have no comparison for an Amiga 3000 with a 50 MHz '030 chip as originally mentioned, but I did have an A1200 with that chip for a short time, only to still think that the A3000 with the 040 was still faster.
