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Hidden duck type: (Australian?) SPOTTED.

Hidden duck types: (Australian?) SPOTTED. LESSER.

Partial answer

As pointed out by Duck, there is

A duck is a bird. There is a train called Duck in the "Thomas the Tank Engine" series. [EDITED to add:] Apparently that isn't the poster's intent, so here's another: the DB Class 403 train, also known as "Donald Duck". [EDITED again to add:] Apparently that isn't the intended answer either, so here's another: the Mallard, fastest steam locomotive ever made. The thing used in war is probably a DUKW. The autopsy might be the abbreviation DUC for "death by unnatural causes". [EDITED to add:] But apparently it isn't; there's a hint about it but I haven't figured it out yet.

Eight words, six references: if exactly one of "white-faced" and "black-bellied" is considered a single word, then we have six hidden duck-types and eight words naming them. Or perhaps the references are things like Duck the train, "duck" the term of endearment, etc., but while I don't have more than six of those so far (bird, train, DUKW, zero runs, "dear") it feels as if there should be more than one more. Obviously the fowl is a goose. Er, no, I mean a duck. I'm annoyed at not yet having solved the Riley.

As pointed out by Duck, there is

A duck is a bird. The Mallard was the fastest steam locomotive ever made. The thing used in war is probably a DUKW. In comments nikki points out that there is a TV show called NCIS in which one character, Donald Horatio "Ducky" Mallard, is responsible for performing autopsies.

Eight words, six references: we have seven hidden duck-types so far, unless MALLARD counts as a "word" as well as a "reference". I think the "references" are things like the Mallard train, "duck" the term of endearment, etc.; I have exactly six of those so far (bird, train, DUKW, autopsies, zero runs, "dear"). The fowl, obviously, is a goose. Er, I mean a duck. I'm not sure what to make of hints 4 and 5 (partials, conjoined, feast). I've got the Riley. Hint 7 doesn't seem like it actually says anything. Hint 8 refers to the fact that NCIS is a Navy agency. Hint 9 is a giveaway for the same part of the puzzle; David McCallum is the actor who plays Mallard.

History:

Some things I thought in earlier versions of this answer: my first guess for the train was "Duck" in the Thomas the Tank Engine children's books; my second the DB Class 403 train, also known as "Donald Duck". I thought the autopsy thing might be DUC, abbreviating "Death by unnatural causes".

Partial answer

As pointed out by Duck, there is

an acrostic yielding ALABIO, our first hidden duck breed.

Now let's turn to the individual lines.

After the last one, let's start a new canvas; back to the solving, we all need some practice.

Hidden duck type: CANVASBACK.

Less erratic the challenge, but words you must spot; tedious, frivolous, dumbfounded plot.

Hidden duck type: (Australian?) SPOTTED.

Approaching the end, but head to the west; Indians have hints, at puzzles, the best.

Hidden duck type: WEST INDIAN (whistling).

Black belly, white face, solve this with grace; prefix to scar, the suffix bled in a race.

Hidden duck types: BLACK BELLIED (whistling), WHITE FACED (whistling). Looks like this is where the embedded Riley is, but I don't have a solution yet.

I'm a bird, yet a train, used in war, just the same; a lot to find here, autopsy my game.

A duck is a bird. There is a train called Duck in the "Thomas the Tank Engine" series. [EDITED to add:] Apparently that isn't the poster's intent, so here's another: the DB Class 403 train, also known as "Donald Duck". [EDITED again to add:] Apparently that isn't the intended answer either, so here's another: the Mallard, fastest steam locomotive ever made. The thing used in war is probably a DUKW. The autopsy might be the abbreviation DUC for "death by unnatural causes". [EDITED to add:] But apparently it isn't; there's a hint about it but I haven't figured it out yet.

Out for a zero, just ditch the bat; dear, there is nothing, left in my hat.

When a (cricket) batsman is dismissed without making any runs he is said to be out "for a duck". (I think this derives from the use of "duck egg" to mean zero, because of the shape.) "Duck", like "dear", is an affectionate term of address in some places. My guess is that "nothing left in my hat" is just referring to those duck eggs again, but I could be wrong.

Hints:

Eight words, six references: if exactly one of "white-faced" and "black-bellied" is considered a single word, then we have six hidden duck-types and eight words naming them. Or perhaps the references are things like Duck the train, "duck" the term of endearment, etc., but while I don't have more than six of those so far (bird, train, DUKW, zero runs, "dear") it feels as if there should be more than one more. Obviously the fowl is a goose. Er, no, I mean a duck. I'm annoyed at not yet having solved the Riley.

Partial answer

As pointed out by Duck, there is

an acrostic yielding ALABIO, our first hidden duck breed.

Now let's turn to the individual lines.

After the last one, let's start a new canvas; back to the solving, we all need some practice.

Hidden duck type: CANVASBACK.

Less erratic the challenge, but words you must spot; tedious, frivolous, dumbfounded plot.

Hidden duck type: (Australian?) SPOTTED.

Approaching the end, but head to the west; Indians have hints, at puzzles, the best.

Hidden duck type: WEST INDIAN (whistling).

Black belly, white face, solve this with grace; prefix to scar, the suffix bled in a race.

Hidden duck types: BLACK BELLIED (whistling), WHITE FACED (whistling). I think the prefix is MAR and the suffix (simply) BLED, so that MARBLED is a third hidden duck-type here. If the "race" has significance, though, I haven't spotted it.

I'm a bird, yet a train, used in war, just the same; a lot to find here, autopsy my game.

A duck is a bird. There is a train called Duck in the "Thomas the Tank Engine" series. [EDITED to add:] Apparently that isn't the poster's intent, so here's another: the DB Class 403 train, also known as "Donald Duck". [EDITED again to add:] Apparently that isn't the intended answer either, so here's another: the Mallard, fastest steam locomotive ever made. The thing used in war is probably a DUKW. The autopsy might be the abbreviation DUC for "death by unnatural causes". [EDITED to add:] But apparently it isn't; there's a hint about it but I haven't figured it out yet.

Out for a zero, just ditch the bat; dear, there is nothing, left in my hat.

When a (cricket) batsman is dismissed without making any runs he is said to be out "for a duck". (I think this derives from the use of "duck egg" to mean zero, because of the shape.) "Duck", like "dear", is an affectionate term of address in some places. My guess is that "nothing left in my hat" is just referring to those duck eggs again, but I could be wrong.

Hints:

Eight words, six references: if exactly one of "white-faced" and "black-bellied" is considered a single word, then we have six hidden duck-types and eight words naming them. Or perhaps the references are things like Duck the train, "duck" the term of endearment, etc., but while I don't have more than six of those so far (bird, train, DUKW, zero runs, "dear") it feels as if there should be more than one more. Obviously the fowl is a goose. Er, no, I mean a duck. I'm annoyed at not yet having solved the Riley.