OK, I'm going to take a crack at resolving the henge issues by proposing a Unified Theory of Henge in the hopes that we can find a way to preserve henge's important role in the setting without causing all manner of problematic implications.
Please spot any issues and ways those issues might be fixed. This is of course all fantasy nonsense, but it should be as internally consistent as possible while producing the desired results for what henge can do.
The theory:
When someone henges into the shape of another person, they're using chakra to temporarily stretch and compress their bodies into the desired shape by moving their chakra pathways around and holding them there, and putting a chakra construct on top of the reshaped body of whoever they want to create the illusion of the right skin and clothes. This extends to giving a person different apparent mass because the laws of physics are being told what the properties of a thing should be by the way chakra flows through it. Change the chakra around and you can change how everything else interacts with it by extension.
However, a person's body is still there, just warped and molded like taffy. They still need to breathe, eat, excrete, and so on. Getting stabbed or poisoned is still a problem because henge can't glue damaged tissue back together, only temporarily warp what you've got into a different shape and slap a construct over it. The constructs are only imitations of real things, so something like creating construct air in your lungs won't help because it's not actually oxygen, just stuff that temporarily takes up space.
Henge construct clothes can be manipulated, taken off, and so on, and they disappear when the henge is released.
When someone henges into an object, the manipulation is much the same as a human but more dramatic. They warp their chakra into the desired shape, slap a construct on top of it, and freeze the pathway flows to imitate the physics of an inanimate object.
Human henges are possible because humans are familiar with how human chakra pathways are supposed to flow. Object henges are possible because the pathways in objects don't flow at all. Animal henges aren't possible because living, flowing chakra pathways are really really complicated and doing a non-human one is just too complex and unfamiliar.
The old henge technique that didn't collapse when subjected to significant physical stress incorporated an additional technique to 'tie off' the chakra pathway alterations in order to make them self-sustaining and not prone to springing back into their natural shape. (Which is what's going on when a henge is popped. Holding a henge is like holding a spring out of shape with your hands. Let go or have your hand jostled enough that your grip slips and it violently jerks back into the shape it wants to have instead of the shape you stretched it into.)
Here are the answers this theory of Henge produces:
- If it's a chakra construct, is your physical body inside it or shunted off to another dimension or what?
- How dense are you when you're henged? More or less than normal?
- Any apparent density appropriate to the person or thing being imitated.
- If less dense than normal, does that mean you get a stealth bonus because your footprints aren't as deep / you don't exert as many newtons on things that might creak / etc?
- Imitating living chakra flows is hard so you're limited to human bodies that are physically viable. You could make a skinny version of yourself, but you can't henge a version of yourself that weighs less than a living human could possibly weigh.
- Can you eat or drink?
- Can you be poisoned?
- Can you excrete?
- Can you suffocate?
- Can you catch a disease? Will the disease still be there when the henge pops?
- If an eyelash naturally falls off, does that break your henge?
- No, it's a chakra construct and sticks around until the henge ends.
- If a hair naturally falls off, does that break your henge?
- If someone pulls one hair out of your scalp, does that break your henge?
- No. The construct is pretty delicate, but it takes a bit more force than that to disrupt it.
- If someone pulls a thread out of your shirt, does that break your henge?
- How about if it's just one fiber?
- If one fiber doesn't matter, what happens if you pull the entire suit of clothes apart, one fiber at a time?
- The pieces stick around until the henge ends.
- If you clip your nails, does that break your henge? Does it matter how much of your nail you clip off?
- Can you integrate material back into a henge -- e.g., sewing a patch on a henged shirt without popping it?
- Yes. When the henge ends you'll just have the patch.
- Can you take off your henged shirt? Does it matter if you're still touching it?
- Can you henge into a person who is 50' tall but not very dense so the mass stays the same? How about 1" tall but super dense?
- No, you're confined to human bodies that are biologically and physically possible for someone to have because it's not possible to warp moving chakra pathways beyond those limits.
- You're carrying a bunch of gear and you henge into a form that is naked. Can you still get to the gear?
- No, it's stuck under the the chakra construct. Also, the amount you can hide is going to be limited because you can't change the gear's mass or volume, only your own. Clothes but not a lot else. If you have a lot of gear you'll probably need to take it off first.
- Where do the things that you're wearing/carrying go when you henge?
- A small amount of stuff can be hidden under the chakra construct layer. It's sort of like wearing layered clothing.
- Can you henge away seals?
- Can you henge seals into existence?
- You could transform into something that looked like a seal, but it wouldn't be functional.
- Could you henge away Zabuza's sword?
- No, you can't alter real objects because henge operates by changing your own chakra pathways.
- How about Asuma's chakra-metal knives?
- How about a summoning contract?
- You could transform into a fake one, but it wouldn't actually work.
- In order to be affected by a genjutsu the user must (normally) be able to see your eyes. Do henged eyes count?
- Eyes you're using to look out of count.
- If you're bleeding and you henge into a non-bleeding form, are you still bleeding inside the henge?
- If you're drowning, can you henge into yourself except with oxygen in your lungs instead of water?
- If you're in a poisonous atmosphere or a vacuum can you keep henging into "myself-with-oxygen-in-lungs" in order to not be affected?
- Can you henge into yourself but with six arms? Or a tail? Or a forked tongue? Or eagle eyes so that your eyes work like a telescope? Or yourself but with eyes in the back of your head as well as the front?
- Can you henge into a smarter version of yourself?
- Can you henge into yourself with a Wakahisa chakra system?
- No. Crippling it that badly takes actual surgery. It won't bend that drastically on its own.
- If Keiko henges into a copy of Hazō, does she get to use the Iron Nerve?
- No, bloodline limits are too complicated to imitate.
- Can you always exactly reproduce a henge you've used before, or do you have to worry about maybe not getting the details right?
- Screwing it up is possible, yes. Practice and a mirror helps.
- Are henges strong enough to last through sex? How vigorous can the sex be? (Assume all parties are adults.) Does it make any difference if...how to put this?...if there's no "tab A into slot B" action?
- Yes. As long as you aren't injured. No.
- If henge can survive sex, can you get pregnant if you have sex while henged?
- Only if you're actually female.
- If you're drunk, can you henge into 'yourself without alcohol in your blood'?
- If you're hungry, can you henge into 'yourself, but with food in your belly'?
- If you're tired, can you henge into 'yourself, but not tired'?
- What happens to your physical body while you're henged? Does it continue to age? If not, how does it form memories?
- If I can henge into people and objects, why can't I henge into animals?
- Non-human living chakra pathways are too unfamiliar and complicated. Doing different human forms is hard enough. Maybe someone might conceivably figure one animal form out with lots of work, but it'd be really really difficult.