Why is "tomate" not plural? Is it customary to use singular nouns when referring to the amount of whatever that noun is (e.g "cinco quilos de fruta" vs "cinco quilos de frutas")?
yes, that's the we refer to it: 2 kilos de batata, 500 gramas de pepino, etc.
Why not "in all" or "all together"?
She buys a total of five kilos of tomatoes - is better English. In total is not an expression that I see or hear in English. It's too literal here.
Does it have to be "no total." Would it be incorrect to say "ela compra cinco quilos de tomate em total."
Not in Portuguese. It's just the way we refer to that. In total = no total