In my opinion, the cargo fly is a must if you are going to do any sort of overnight trip, or any paddling carrying gear. Having a pack on the bow is actually a much bigger deal in flat or open water than it is on a river. Not only does it increase the boats (already considerable) wind resistance, it makes self rescue more difficult in a situation where you can’t just swim to shore.
It is also much, much easier to keep your sleeping kit etc dry inside the boats tubes than in a pack on the bow.
Yes, the cargo fly zipper has to be maintained, but it’s not high maintaince. I’ve had it covered in some hedious sand, mud and silt, and it still worked. IMO your repair kit must include a stiff bristled toothbrush, a water bottle nozzle that allows a “squirt” and zipper lube. If you have those, it will work forever.
But the real take away is to look at packrafters like Roman Dial, Brad Mikaljohn, Luc Mehl and Mike Curiak who were around before the cargo fly. None of them are paddling fly-less boats.
If the cost isn’t prohibitive, there’s no major downside. If you never open it, you never have to maintain it. But it will be there if you want it.
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