Until recently 9mm ammo was extremely cheap.
Now of course, the issue is 'what is available' instead of what is affordable.
Since handgun shooters 'generally' shoot a lot more rounds to develop proficiency than riflemen, cost is an important issue.
On-the-Other hand, if you can afford to buy ammo for a .45, or if you get into reloading (recommended), then I don't see any particular advantage to a small bullet hole compared to a large bullet hole.
If notthing else, you can see the holes in the target easier when shooting a .45.