example:

/routing ospf interface set disabled=yes

compare to

/system ntp client set enabled=no

Should everything be standardized on enabled/disabled - at present, some things seem flipped and could cause people to set the wrong thing in configuration?

It kind of is standardized.
set disabled=... is used for items that can be added to the list.

set enabled=... is used to enable like servers. example:
/mpls ldp set enabled=yes
/system ntp client set enabled=yes
and so on.