Which is weird, considering that traditionally Lycanthropy, Vampirism and Lichdom are always acquired conditions. I can't see how they could not be templates...
And see, back in 3e, I would have agreed with you. Since NPCs were built the same as PCs, and all NPCs had classes, it made sense. Create the character, add the template.
But in 5e, NPCs aren't built like PCs. They're purpose-built, like monsters.
So if you just want a "regular" werewolf, one built on a normal/average human (or elf, or whatever), that's represented by the one in the MM. If you want something more specific--a werewolf mage, for instance--then you use the rules for modifying/advancing monsters.
If you're purpose-building the NPC
anyway, the template doesn't save you anything.
Or the lich, for instance. I'm sure making it higher or lower level is an easy enough modification, and otherwise it's just a matter of swapping out spells. Again, if you want something
way out there, you'll need to build it from the ground up--but you'd have needed to purpose-build the base character from the ground up anyway.
This is all assuming I understand everything correctly, of course. But if I do, it'll work much like it did in 4e, and monsters in 4e, for the most part, were pretty easy and smooth to build and work with.