Not using C# tho just means you are isolating yourself. You will have trouble with guides, tutorials, using OSP code, asking questions, etc. Using the tool that everyone else uses makes things easier for you as well.
devs didnt release the modding tools yet, which includes the game code. So you can expect things to change when that happens, including how C# is used.
it also doesnt matter if you use hooks or not. Its the same as using hooks with C#. If the code changes, and it will change a lot for EA, things will continue to break often for mods. You need to support a version and stick with that, not the live one. Eventually the game will stable and the API should also be stable enough that mods wont be fragile.
and when we get total conversion modules that will not be a problem, as they will just have the game code (not the engine code) with them, so it is very unlikely that updates to the Native game would break them.