yes....in hindi the singular and plural word for apple is the same....hence सेब can mean apple or apples
Could this also be understood as "water and an apple," or would that require an explicit "aik"?
Yes, my question has to do with the word alone. If I see "aik kitab," clearly that means "a book," not "the book." If I simply see "kitab," as in "vo kitab partee," could this be either "the book" or "a book"? If so, when should one use "aik kitab"?
If you simply see किताब, it can mean both a book and the book.
वो किताब पढ़ रही है can mean -
She's reading the book.
She's reading a book.
As for using एक, you should use it whenever you would use it in English. There is no harm in using it and it only makes your sentence less ambiguous.
If my sister asks me -
क्या कर रहे हो? What are you doing?
I could reply with - मैं किताब पढ़ रहा हूँ or मैं एक किताब पढ़ रहा हूँ and both would convey the exact same meaning.
Since Hindi doesn't have the equivalent of 'the', you'll have to make do with 'that'. मैं वह किताब पढ़ रहा हूँ जो तुमने मुझे दी थी। I'm reading the book that you gave me. Here वह refers to the particular book that was gifted.