Vocabulary
 

Are they both correct?

-In our language, the official language is X and we have dialects Y and Z. When we write in written language in X, Y or Z, they are almost the same, though vocabulary is slightly different.
-[...], though vocabularies are slightly different.

Both are fine.

...though vocabulary is slightly different. (Looks at X, Y and Z's shared collection of words as an almost all-inclusive unit with only small variations needed to tailor it to each separate dialect.)

...though vocabularies are slightly different. (Looks at the words of X, Y and Z as separate collections that only differ slightly between each other.)

Thank you.