In this sentence 'the 'boys' want 'their' dessert now' do the italicized pronouns agree in number with the italicized antecedent or antecedents?

"The boys want their dessert now."

Yes, the possessive adjective 'their' agrees in number with the plural noun 'boys'.

The pronoun 'their' is the plural form used to describe a noun belonging to a plural noun (or two or more nouns).