Speaking from personal experience, and having been confused by this duplication
in the past, the problems as I see them are:

a. More than one way of doing things. This means that there is duplication
between the hook_something() and hook_nodeapi('something').

b. This duplication causes confusion to many developers (myself included).

I will leave others to comment on the details codewise, but here are the options,
in order of (my) preference:

1. Restricting node hooks to one way of doing things (hook_nodeapi). This means
deprecating all hook_something() for node operations. This way there is no confusion.

2.  Eliminating all the hook_something() that are duplicated by hook_nodeapi('something')
and do not suffer the drawbacks listed above. This may mean leaving the node_load()
hook, and maybe others, and that is fine by me. Less confusion.

2a. Same as 2, but eliminate the nodeapi('something') that has an indispensible hook_something()
equivalent. This way we are back to one way of doing things.

3. If the present scheme MUST stay as it is, then I don't know if documentation improvement will
be enough to overcome the drawbacks.

Other ideas?