If you switch off the option which hides Player buttons in automation mode, the Hook and Loop buttons remain active in automation mode, (although they seem (?) to have no effect).
BFN
CAD
I would love to take a look, but Vista decided that it was time to reboot and configure updates while I had left for dinner. Writing from my MacBook right now.
It’s not a bug actually, because the buttons are just shortcuts for the respective player options which you can still modify through e.g. the context menu even when automation is active.
Hook Mode does work in automation, apparently Loop does not, but I think it should.
I see what you mean: they can indeed both be set from the Player’s context menu in Automation mode.
I can see an obvious problem if Loop mode is allowed during Automation :D, but for consistency’s sake, I agree with you. It’s just a bit of a pain to discover that Player Loop/Hook buttons (if made visible) do work in automation mode, given the job I’m doing right now … 
BFN
CAD
PFL does as well (if “independent PFL” is switched on). So, in principle, the left hand buttons do work, while the right hand buttons do not.