I’ve noticed anime series often tend to appear allegorical at first and then either veer into superficiality (which isn’t a bad thing in of itself) or fail to deliver anything other than tired pop philosophy platitudes that don’t ruffle any feathers.

You have to consider anime are mostly manga and light novels adaptations and the choice very heavily influenced by popularity and you guessed it popularity among certain demographics is incredibly simple to define.

How do you write something with a deep message about our world that isn't just "Japan society sucks, you suck because you are all apathetic cowards that don't want to organize or care about politics, also you have incredibly deep rooted problems with authority and conforming with the status quo, [add another 20 criticisms here]"?

You can't write that without being cancelled, parody and cynicism is fine and there are many examples of it, but actual political messaging is never going to get through the filters. Really remember that manga specificaly have to go through a filter, before you even get published you have to go to the magazines and basicaly pitch your series with a first draft(forgot the proper name).

Basicaly while I am sure many Japanese know all the problems but there is a huge barrier to voicing a message that reaches a large audience.

And the whole light novel/doujinshi side of things is basically a lottery and most people would rather gamble on what is likely a winning choice(i.e write a popular genre).