A situation doesn't have to be explained to have some kind of workable explicability. And if you don't have the latter, yes, what you generally have is bad writing.
But you do get an explanation: Kirk is immature. It's right there in the film when Pike relieves him of command.
"Natives who have barely invented the wheel see a starship rising up out of their ocean!"
Do we need Kirk to explicitly explain why he hid the Enterprise down there? We know it's a bad idea from a technology standpoint as Scott is complaining about it, we know the entire situation is dangerous from the bridge dialogue and we know that it shouldn't have happened from Pike's dialogue.