I don't think this is correct. The output in the commands listed contains all hooks, server and mom, I think either the top level hooks/ directory should remain with qmgr_ph_default.out and qmgr_lpbshook.out in it, or those two files could be moved to server/ (because mom hooks are configured via the server). I prefer the top level hooks/ directory.
As for the actual hooks directories in server_priv and mom_priv, for mom_priv why not just follow how server_priv is currently defined in the EDD, since as it is written already hooks/ will be copied in?
I think it is fine as it is. Adding another layer just means more typing to get at the same information without adding to the overall organization. Others may of course disagree, and if so please speak up.
One more thought is that currently we have qmgr_lsched.out at the top level rather than in a scheduler/ directory. That makes some amount of sense because currently that's the only relevant command output. Once PP-748 goes in, will we need more, like "list fs_group", "list policy", "list time_window" (that may be a question for @jon and @arungrover , and probably added to the WIP PP-748 EDD as far as what gets listed or not listed when doing "list sched")? I would suggest creating a scheduler/ directory now and putting qmgr_lsched.out in it and we can add to it later as needed.