Just like Whatsapokemon said, it is all about knowledge. If you see a pony in the show or on a picture there are almost always not enough informations to identify the complete anatomy. And not everyone knows the (not completely realistic!) anatomy of ponies by default. Most people even don't know human anatomy. And most people also don't know about other everyday things like how a computer works, physical relations and so on.
Additonally, every brain is different and not everyone can analyse or understand a construction (like a pony e.g.) just from the beginning by only looking at it. I bet you encountered difficulties as well with other things like perspective, lighting or something completely unrelated to drawing. That's just normal diversity.
I wouldn't really call it a stupid question. The answer may be somehow obvious, but on a second look can be complex and lead to new perspectives. And new questions. So these "why" questions absolutely have their right to exist. Not only for me as a budding natrual scientist, but for all those important things in life that you already mentioned.
As for me I was always good in technical drawings including perspectives, but struggled a bit with organic shapes. Redraw what I see was not a problem (especially when it is our fat tomcat ^^), but creating own natural and organic shapes felt pretty difficult. Always interesting to see this distinctions and contrasts.
Thinking about the "why" is difficult and needs the will and ability to allow other opinions and ideas (at least for the time of the analysis). Indeed a lot of people seem to be overstrained by this (and sometimes there is just no reasonable explanation). One of the reasons, I think, why tabloid press is so popular.
But we wander from the subject that initially was drawing ponies.