I've just installed Hierarchical on a test site with Pods installed.
Using the options in Pods admin ( Advanced Options > Post type options ) I was able to change the slug but the check box option for hierarchical ( already set to false ) doesn't seem to have any effect.
I have a long list of test CPTs already so hiding them in the nested Content view would make sense. I guess they should have been hidden from the off.
Checking and un-checking the option in Pods ( and saving ) doesn't seem to have any effect.
Will this only work if I hard code my CPTs via functions.php?