That second 了 is the sentence-final 了 (了2), separate from the 了 right after 吃, which is the verb-completion 了 (了1). You actually have two different 了s doing two different jobs.

吃了 marks that the eating of each apple was completed. The 了 at the very end tells you the situation holds up to now — it adds a sense of "so far" or "up to this point," and often implies the action might continue.

Compare:

• 我吃了三个苹果 (wǒ chī le sān gè píngguǒ) — "I ate three apples." A flat statement of what happened, finished, no implication about now.
• 我吃了三个苹果了 (wǒ chī le sān gè píngguǒ le) — "I've eaten three apples (so far)." This suggests you're still eating, or that three is the count as of right now, and could change.

This double-了 pattern (V了 + number/amount + 了) is very common when reporting a running total: 他学了两年中文了 (tā xué le liǎng nián Zhōngwén le) — "He's been studying Chinese for two years (and counting)." Drop the final 了 and it just becomes a closed statement about the past, with no sense of continuation.