it seems that they made a few attack sprites for different types of attacks and made two sprites per weapon/hand that would fit where it should. i say two, because depending on the direction, the weapon/shield sprite should be drawn over the player sprite (if weapon should be seen in front) or under (if seen in behind). here's an example:
is made up of:
(i had a hell of a time fighting with my image manip programs. i almost had it with proCreate but the layers were going all see-through and stuff. it was retarded. then i was dumb and saved out as jpg and it made a mess of the images. then i was even dumber and couldn't get psp3 to paste an image over another and have transparent bits not show. been a while.. )
so here, we have the cardboard tube at that view as being in behind the monk sprite. isn't there going to be another sprite for the cardboard tube that would just be a fully transparent sprite? well, that seems silly, doesn't it? why not just tag the view for that angle as in front or behind? that makes more sense, come to think of it. i was thinking there would be a point where you'd need to have it in front AND behind - but what would ever be that way that couldn't be altered?
in secret of mana, its pretty obvious. they drew a series of weapons doing their attacks, walks and idles, and then made the character sprites fit the weapons. every character holds and uses every weapon exactly the same. it certainly isn't going to be very easy to do differently sized characters, but you can make the animations much more generic.