Configuration node prevent-shop-creation-item-regular-usage: true doesn't working!
I want to protect shop creation from players, but they anyway can create shops using spawn egg!

This setting is for preventing 'regular usage'. For spawn egg that means that it doesn't spawn mobs anymore.
There is currently no option to disable the creation of shops via item, however you can achieve that by simply changing the shop creation item to something that players will never be able to get (for example an item with very specific lore).
If you want to prevent players from creating shops at all, you can also use a permissions plugin and remove the corresponding permissions (see here for all permissions: https://github.com/Shopkeepers/Shopkeepers-Wiki/wiki/Permissions).

That will remove the hiring permission. To prevent players from creating shops, you will have to remove shopkeeper.player

See the wiki on that: https://github.com/Shopkeepers/Shopkeepers-Wiki/wiki/Citizen-Shopkeepers

Yes.