Not being a Mega ST owner, I can't comment on the first question, but there are pictures around of people who have Goteks and Lotharek HXC floppy emulators in their ST's. I've also seen many pics of Amiga owners doing this although I don't own anything Amiga. The Ultrasatan can be used externally with an ACSI cable. I have an external cased ultrasatan with the ACSI cable, but I have been thinking about selling the ACSI cable and case and internalizing the UltraSatan. If aesthetics (not hacking up the case) is your primary concern you might be happier keeping it external.
I would assume the fan could be replaced by any modern PC case fan? Just measure and see if it's mountable the same way case fans are. If it is, you can get a nice fan that pushes lots of air without making too much noise cheaply.