There are some differences but these seem to be very special. I can run a Workbench superfast on my small Notebook - much faster than my 040/40 Amiga 4000 - but I can really not use DigiboosterPro Music Tracker on the same Notebook. The software works, but stutters and sucks while playing mods. Even with only four audio channels. My real Amiga can do much more channels. Even the old Protracker has this issue for me.
Another difference is of course the whole nostalgic thing. Maybe it's comparable to listeing to vinyl records. They are not really better and do not sound better, but if you are into it, it is so much better
But there is nothing to say against emulating. I do it, too. We are all guilty
Sometimes it's just easier und more convenient to fire up the emulation on the raspberry pi on the big tv screen and play Lotus 2.