Well, even in core MM, you can find 5 incorporeal undead creatures. And one is template, and other two have variant (Wraith/Dread wraith, Shadow/Greater Shadow). This is only slightly above 1% of the entire monsters in MM. But actually, those creatures are quite popular in many published (or otherwise written) adventures.
if you read official modules, you will notice that there are so many encounters against incorporeal undead creatures at any level. In my understanding, they are popular because,
1. Undead
Indeed. Undead monsters are so popular at any level. Many of the DnD adventures involves closed dungeon environment, And Undead monsters (basically) exist forever and don't need food or water.
2. Stands out
Even amongst undead monsters, they look special, Thus loved by many authors and DMs who love to include some "different" encounter or two.
3. Effective against higher level PCs.
You will not see many CR 3 creatures, say worg or ogre, in many adventures designed for 10th-level party, even as minions of BBEG or grants of med-class- bosses. But you will see Shadow (also CR3) in many of such adventures. While usual creature of that CR are not threat at all to the characters of that level (even as a supporting soldier), shadows can often do some damages to even a 10th-level fighters and such. And because of incorporeality, they survive many attacks, both physical and magical ones. So, you tend to see many low-CR incorporeal undead creatures than other creatures of the same CR.
4. Villains can summon!
Supplements introduced Summon Undead spells and there are classes and monsters (like nightshades) who can summon incorporeal undead. And, because of the reason (3), incorporeal undead monsters are good choice for summoning.