In the context of SDS/MSDS's my understanding is it's more about proper disposal. In the event you need to dispose of it, a fragrance oil labeled as toxic to aquatic life shouldn't be poured down the drain- you'd need to follow local guidelines for proper disposal of hazardous waste. When diluted properly into a finished product it's essentially the same as any other scented consumer product and doesn't need special handling.
It can certainly be debated whether any of these chemicals, whether from synthetic or natural sources (plenty of EOs have the same warnings) should EVER be going in our water- it probably depends on the chemical. On the one hand, "the dose makes the poison" as they say; on the other, some chemicals persist and accumulate and some may have unforseen effects, and we don't necessarily have all the information. That ultimately leads to the question of whether fragrances should be used at all, and I don't think there are easy answers. Personally I'd like to see a lot more transparency from manufacturers so we could make responsible decisions with more information. But I don't see that happening on the scale that would be required.