Doduo and Dodrio do have wings IIRC, but they're really small and aren't used for flying. If they learn fly anyway, well, it's no less weird than Rattata learning Thunderbolt. Also, the reason you can't see them realistically is because it blends in with the rest of the fluffy feathers, and then literally because Game Freak doesn't like to take a whole lot of artistic liberties with Pokemon beyond the Sugimori standard for some reason. Instead, they'll play the "fans use their imaginations" card.
It's okay to show Doduo with its wings outstreched, guys. You won't be sent to prison.
Ice Punch plus Wooper, simply put, Wooper uses its tail. Using the definition found here:
https://www.merriam-webster.com/dictionary/punch
Punch when used as a verb, the second definition, states that to punch is to strike with a forward thrust, especially with a fist. It didn't say exclusively with a fist, though.
I've never heard of Dragon Pulse, so that depends on what the move really implies.
Gastly probably can form temporary hands with that gas around him, or at least make the gas around him dense enough, and then compact it into something to strike you with. That or he uses his tounge. Gastly seems to have shape shifting capabilities anyway, or at least the power of illusion.
If nothing else, Pokemon Mystery Dungeon has a Diglett mentioning that it has feet. In the off chance that it doesn't have hands either (which I doubt, but again, GF loves the "use your imagination" cop out), Diglett/Dugtrio jump out of the hole and use the claws on their feet. Of course, if they have hands, it makes more sense because I don't see moles exerting all that energy just to use one move. So, they just Slash with their foreclaws instead. See Duduo for why you'll never see it officially.
Zubat can probably do a non literal Mean Look by contorting its face enough to be bone chilling. It has a mouth and fangs. If it can work up a nasty snarl, I'm sure the opponent would be in no condition to think on its feet.
Attract is all about manipulation using some kind of means. How it works, I have no idea, and can probably be taken to places no one wants to go, but the point is that it's insincere. Jynx using Attract doesn't mean she's coming on to the opponent, it just means she's bewitched the opponent using whatever she has at her disposal that puts the opposition under that spell. Two different things. Also, I find it hard to believe every last Jynx looks the same anyway, especially if they've been manipulated with Pokeblocks and whatever else, which instantly guarantees that they don't.
Don't know a thing about Arceus, no answers there.
Rhydon is the only one I can't really give an answer for unless it being a rock type is purely metaphorical. I forgot if its armor is made of literal rocks. Having said that, it could probably still swim if forced to. I mean, it's not going to just give up and drown if dunked into water. It'll probably swim slowly, though, just to keep impact low. So even if you could surf on Rhydon, I'd imagine the trip would take forever, and you'll have wished you taught surf to a proper water type instead.
:D