Today's situation with the lot being at capacity is a rarity. When you consider that typically more guests arrive by Disney bus to the water parks, the onus to explore paid parking simply isn't there. The theme parks see far more guests per day, including more guests arriving by car (and being subject to the parking fee) than those who arrive by Disney transportation.
None of that matters - what matters is if the opportunity being worth it... not comparisons to what the parks do. The water parks still have large amounts of car usage, even if it's not as large compared to the main parks.
To your point about automation, that's also a non-starter. Disney does not want to be in the business of giving "parking tickets" for failing to pay at the kiosk or on an app, and automated gates like what you'd see in an urban parking garage also wouldn't work because of the morning volume.
One "boomer" not understanding that he has to insert the credit card and remove it quickly could cause a massive backup.
Parking tickets? It would be fixed price, so you pay at entry... or they could do something to pay at exit to avoid backups at park opening.. since people tend to leave at much more spread out patterns (except in the case of a weather closure) so simply collecting at exit is a much easier on traffic - but flips your staffing demand pattern. Any automation could be augmented by 1-2 staff assisting guests who get stuck. This is easily solved.
Basically there are a ton of ways Disney can do this that are all well established... virtually every regional park in the country has figured out how to do this... Disney not charging is the exception, not the norm.
It's all far more trouble than it's worth at this rate. The water parks see a fraction of the guests the theme parks do, and even the theme parks drop the auto plaza staffing around two hours prior to close.
You keep bringing up this stop collecting parking at the end of day thing as if it's significant or comparing with the parks. The whole point about the end of the day is the traffic pattern makes that period insignificant and why they do it. That has nothing to do with the decision of if you charge for parking or not.
That said, they certainly could add a parking fee. But why not jack up the price of the water park ticket by $10 per person and maintain the status quo?
Same reason all amounts are put into one bucket or another.. manipulation and marketing.
For perspective, it costs $30 to park at Aquatica. Even if it were only 500 cars a day at a Disney water park.. that is nearly 5.5 million dollars a year in revenue assuming one water park is open.
Do you think Aquatica is achieving the impossible or is losing money by charging for parking? Or is it simply possible to do, but Disney choses not to... just like they never used to charge for hotel parking... until they simply decided to.
Aquatica simply has 3 double lane booths at it's entrance - it's not some complicated thing.