In English, "remain" is a state verb, describing the current state, so it's natural to think that the Korean word 남다, often translated as "remaining", is the same.
However, I think it's best to think of it as an action verb, "to leave over". Then:
사과 4개 남았어요
means that 4 apples have been left (and are therefore remaining).
Another example would be the phrase "남은 밥". Since 남다 is a verb, 남은 is the past participle, and so 남은 밥 means the rice that has been left over - someone didn't eat it, they left it1.
In the example 9초 남았습니다, this is a bit less intuitive, because there is no agent that is "leaving the seconds over" - but still, they have been left over, it is considered an action that is past.
Note that there are some other Korean words that are sometimes surprisingly found in the past tense, too, like 미치다, 식다 and 늙다. The reason for these is different - they are actually verbs, but they translate to English adjectives. For example, 미치다 is a verb meaning "to go crazy", therefore we can hear:
미쳤어요? (Are you crazy? - Literally, "Have you gone crazy?")
Likewise, for 식다 (to grow cold):
밥이 식었다 (the rice is cold / the rice has gotten cold).
1 남다 is actually intransitive, meaning the subject is the thing that is "left over". The verb 남기다 is the causative, and allows us to say that someone left something - e.g. "내가 음식을 남겼다" means I left some food. If I say "음식이 남았어요", the agent (me) cannot be given, and we focus on what is left over. In the case of 9초 남았습니다, there is no agent - the time is "left over", not elapsed yet - but there actually is no agent that is leaving the time.