Yes, the 3rd person possessive ending is " i " for words that end in a consonant (like kitaplar) and "si" otherwise.
And the accusative ending is " i " for words that end in a consonant (like kitaplar) and "yi" otherwise.
So of course that means, words that end in a consonant have the same form when saying "his/her/their" and when using it in the accusative.
Kitapları = his/their books
Kitapları = the books (accusative)
(In the sentence above, it's the possessive ending. We know this because there is "onların", which means something must be possessed. Besides, only transitive verbs require objects = accusative. "Var" is not a verb, let alone a transitive one. So no accusative is used in this sentence.)