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When having the choice to use a Hook or defadvice to manipulate a certain package, what should you do?

Hooks are always better because they break less. If the author provided a hook, then the author expects user code to run. Advice, however, can have unexpected side effects. Advice should only be used when no hook is provided.

The problem is that advice subtly changes the semantics of the commands it advises, and this change is not visible in the code of those commands. So it works, but it’s better to fix those commands directly. That doesn’t mean `advice.el’ is evil, but that it should only be used when you cannot change the command; for example if you want your package to work with older releases.

What I particularly don’t like about advised functions is that it is difficult to use the debugger with them.

And here is StefanMonnier’s strong ‘advice’ advice from mailing list

    `advice' is a sledghammer: it's the last resort before
    modifying the source code.
    Advising is a source of major headaches because of unexpected
    interactions with other pieces of code...
    Advice have to be written *extremely* carefully.
    I.e. if you can do it without `advice', then don't use `advice'.


Extra special care needs to be taken when advising Emacs Lisp primitives. The special case of advising primitives is further explained in the EmacsLispReference. – YoniRabkinKatzenell

And this is what RichardStallman said 2005-03-03 about Emacs developers (not users) advising Emacs primitives:

    Please do not think of making any part of Emacs advise primitives.
    That technique should never be used, because it causes confusion.  All
    code in Emacs that advises other parts of Emacs was installed without
    my knowledge.  It is a bug that ought to be fixed.


And this is what RichardStallman said 2005-08-03:

    No!  Emacs code should not use defadvice.
    When you're trying to make improvements in Emacs or fix problems in
    Emacs, please do NOT think of defadvice as the way to do it.


And this is from an exchange on, 2007-06-02, between KevinRodgers and EliZaretski?:

    Kevin> I think RMS' position is that defadvice should not be
    Kevin> used within Emacs itself.  But the inclusion of defadvice.el
    Kevin> in Emacs is tacit acknowledgement of its usefulness
    Eli> You are right on both accounts.  And I see no contradiction
    Eli> between those two, because RMS never said that defadvice is
    Eli> not useful.  His position on not using it within Emacs itself
    Eli> is because doing that obscures how things work, which is bad
    Eli> from the maintainability point of view.  FWIW, I agree with that.