It depends on the quality of regulation in your country.

When the regulation isn't properly done or enforced, for example when living above a restaurant you get things like excessive smells (they're supposed to have their own chimney all the way to the top of the building) and higher fire risks (they're supposed to have specific fire safety facilities above and beyond what a normal habitational unit would have).

Around were I am - in Portugal - living above a restaurant being a good thing or not very much depends on the municipality were you're living since some are quite corrupt or just plain incompetent and Justice around these parts is a slow, innefective and unreliable joke.

PS: Mind you, shops on the ground floor of appartment buildings around here are pretty standard, it's just that specifical example of yours of a restaurant might not be such a great thing to live above when the regulations that are supposed to protect everybody else aren't sufficient or aren't enforced. Most other kinds of shop don't really have that problem.

Shophouses are pretty ubiquitous in SE Asia but they aren’t typically MDUs like pictured; more like townhouses. I wonder if that’s the situation in Tokyo too?

https://en.wikipedia.org/wiki/Shophouse

I lived above a pizza shop at one point. Was not an issue.