Sounds like the entering air is drying out solution that is wicked inside the air tube inlet during the ebbs in pressure. Have you checked to see if water or working nutrient solution itself works (by playing around with the orientation of the "Y", to avoid possible drying at the far end where the water can enter? Also shutting the air pump off such as would happen on a timer could repeatedly cause a layer of concentrated salt to form when the pressure relaxes and resumes, which is not easily re-solubilized.

pH down will likely clean it and return it to solution, each time you need to use it, if you can introduce it there without damaging the air pump.

Maybe you could modify it to have larger diameter tubing and fittings?

I've always let the air pumps(eight Waterfarm completes) run 24/7. I quit adjusting the ph three years ago when the c02 generator was installed(didn't see enough of a difference to bother). I mix GH flora series and have backed it off to a 70% mixture(from full strength).
They do sell a kit (Waterfarm) with bigger fittings and stuff but I'm not really sure if it comes with a bigger "y" or bigger diam. air line or anything like that. I got ninety-nine problems and a ----- ain't one.

I haven't used a CO2 generator so I can't be sure how yours might be set up. But if you are using CO2 gas as pH down I would see if there was a way to have a small amount of CO2 entering through the airline if a tee or something similar could be put in the airspace portion before the liquid contacting tee.

Like I said, I don't know anything about how these are set up so maybe that is not possible, but if it is, you would be sure the carbonic acid produced from your dissolved carbon dioxide at the critical "Y" slightly acidifies the area where the deposits are being formed and likely dissolves them, just like in nature (the ocean and naturally mild acid rain).

You sure sound edumacated! Introducing co2 to the nutrient solution? That's a wild idea! Maybe if I was doing my college thesis. No, I'm kind of lazy. If I can't find anything safe to pour in that will prevent this from happening then I'll just continue to poke out the air line with a toothpick every couple months or so.
What sucks is having to lift the plant basket(containing all the clay pellets) out of the bucket to get to it.
When you try to pull the whole works out, the y always comes off halfway up the outer plastic line and then you have to push it back out to get it.
It's a design flaw that haunts me repeatedly. I'm getting a headache thinking about it. Bye for now!

Oh, forgot to mention. Just got an aeroponic cloner. LOVE IT! A not so intelligent child could use it. Nothing stealthy about it though. You can hear the water spraying on the plastic inside of it plain as day. Oh well.
I like using the neoprene inserts. I'll never buy another plug or jiffy pod again...

I've never seen a hobby CO2 generator in a hydro setup. Sounds though like fooling a bit with that sort of thing would be fun on a rainy Saturday, but not for work or school that sounds seriously not like fun. But I'm not sure if I could handle a design flaw clogging up an airline to often either. CO2 wouldn't affect much the O2 already in the air. I'm betting you could preventively just squirt a small amount of pH down acid in the airline after the pump every now and then and it would clean out whatever started caking up.

Good luck with that unique 'rig' that you already could start some R&D yourself!

A feeding diam should always be twice the size of the two outlets or it will cause enough back pressure into the previous manifold producing the source pressure.