[ergocoder]

I've never found anyone who was punished for asking questions / raising concerns about org problems to leadership.

Most of the times the leadership is clueless about the problems in their orgs because nobody wants to tell them any real problem.

They appreciate that you share your pain points with them even without solutions.

Of course, you should share the pain points in a polite manner where you talk about your perspective only without speculation on other people's intents. But you should do that any way regardless of who the listener is.