by the looks of it, it seems that your carp aka kois are eating the leaves. In the past it was fine as the kois were smaller and now, 2 years on, they get bigger. This means that if your feeding did not increase in moderations, they will turn on your plants.
You need to check on your water parameters at all times. As you mention, this is a ecosystem and the main media is the water. You have to check on the PH as well as the KH, Ammonia and Nitrite levels. This is important as your pond is exposed to the weather. With the current pollution in the air plus the haze is not helping as all this pollutants rain into your pond. Since its a close ecosystem, all this does not get washed away.
Plants needs nutrients and condusive environment to grow. My guess was that in the past, your system was able to support the lotus and they flourished. When that happens, an increase in plant population means an increased need for nutrients and they have perhaps exhausted and/or the demand has out stripped the supply.
Fish poop is not all the nutrients plants need and by the looks of the leaves that has gone yellowish, there could be a lack of iron. You need to fertilise the pond.
This is just my opinion based on what I see.
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