You have a point with libraries. I'm not at all familiar with them, so I don't know how a reasonably-well-designed game would use them or how difficult they would be to decompile, modify, and replace.
In any case, I think we all know Mojang's stance on an actual modding API. How many years have they been promising to create one?
It depends on what you use to make it. For things like .Net, which compile into things like DLLs and EXEs, its trivially easy unless you use obfuscation. For fully-compiled languages like straight C++ (I don't know about Qt C++, I've heard it has some form of reflection, but I've not read up on it), such a thing would be exceedingly difficult. However, chances are, that if the hypothetical Minecraft were made in straight C++, then there'd be facilities to at least script your own content, even if proper tools were made unavailable. Again, it has a
lot to do with things like compilation time (something like Minecraft would take a very long time to compile w/o scripting) and the ease with which the original authors can add content. That's something my C++ books drilled into my head from the very beginning: the more complex your project becomes, the more time and resources it'll take to maintain. Its why a lot of games use things like Lua, custom scripting languages, QML, and the like. In the long run, it makes things much,
much easier to maintain.