Well the nematodes are not a bad thing, harmless Panagrellus, in fact the fish should be scarfing them down. Same type nematode people raise for fish food, microworms.
The cap in pic is in no way a 2-3mm cap, unless you have it under that layer I see on top which I’d put at 5-6mm. But even though it may not be proper pore grade for cap and allow humic substances to leach into water column faster than desired that still doesn’t account for what your neons are showing. Neons love blackwater’ish envirements, Rasbora as well. Are Rasbora also showing same symptoms? What is actual substrate you used for cap?
What is actual brand of soil you used? I read in your other post it being Miracle Grow Top Soil but I can not find any product on their page called Top Soil.
But as I gather from your previous threads/post fish were healthy when you brought them home, acclimated well it seems, you built up population of your stock in small increments, your water change routine seems fine for that type tank. But yet even though you’ve pretty much done everything by the book except for maybe not using right size substrate for cap (?) things have gone down hill with fish rapidly in last 2 mo.
Only thing I see that worries me is high PH, the soil should have that well under 7 by now, should probably in 6.6-6.8 range. Soil you used doesn’t have bone meal and other additives in it does it?
Your plants look healthy and thriving, pretty much algae free in tank which is what you should see in blackwater/soil tanks.
What is your water source and what does its PH/GH/KH read after degassing in a bucket for 24hrs?
Can you think of some change you made in tank where after it these problems started?
There’s something amiss here, neons should be healthy, happy and thriving in that type of tank.