This isn't a matter of setting – it's simply because it's an over-used trope. It's a form of lazy writing / lazy scenario design.
In a D&D-genre game where the DM is not trying too hard to present a believable world, they might rely on stereotypes and stock situations with regularity: every cemetery is full of risen dead, every peasant town has sacks of gold just lying around to pay adventurers with, every evil necromancer wears black, every goblin speaks pidgin English, every dwarf is surly and has a Scottish accent, every monster fights to the death, every culture buries their dead instead of cremates them, etcetera, etcetera.
Because of this, the fact that every graveyard you visit is crawling with undead doesn't signify anything within the game world. It usually just means that the DM isn't going to bother putting a graveyard into the game unless it exists to contain undead.
There are ways to combat this trend. A DM can mention graveyards when they're not full of undead, to break the association of graveyard = undead for today's adventure. The DM can also use other locations that spawn undead, such as swamps, ancient battlefields where there was no-one to perform a proper burial, only graveyards that have been desecrated or contain an evil influence, or a necromancer's mountain fastness. They can also just use undead less often, keeping them for special adventures, to make undead appropriately rare in a world where the common people truly have no reason to obsessively cremate the dead.
Basically, there is nothing in the rules or the implied setting that says undead should be as common as some DMs make them be. And often, those very same DMs simply don't bother thinking too hard about what it implies when they over-use undead as a stock enemy. You can make undead common in a world – but as you note, this should have consequences on the rest of the setting if it is going to qualify as a well-craft setting.