The trick is that we don't actually want to shame and anger people posting comments that don't fit into the HN ethos; we just want them to improve their comments, or wander off elsewhere without feeling too bad about it.
If someone has good ideas but is used to discussions on wilder forums, we want to educate them in a respectful way. If someone really doesn't belong here, we don't want to get their attention; we want to make HN as boring as possible to them, so they go away instead of posting a self-righteous rebuttal or seek vengeance in some way.
On the subject of respectful education... it might be helpful to have some built-in explanatory text shown next to downvoted posts shown only to the author, with the standard reasons for HN downvoting, and suitable responses for downvotes that seem unjustified.
Can you clarify the kinds of self-censoring you're doing?
Some of it is really a very good thing -- namely, "am I asking a question that would be trivial for me to answer for myself?"
There are plenty of "stupid" questions that are important to ask of yourself (and are part of the learning process for all of us) but need not clutter up a good discussion.
If everyone self-censors by asking "will this increase the value of this discussion for other readers?", I think that's a good thing.
I think you're talking about self-censoring based on "will this comment reveal my ignorance and harm my karma?", which isn't the same thing. A question or two along the lines of "I don't know much about this, but it's interesting and seemingly not well-covered online -- does anyone want to give a quick high-level explanation?" are normally welcomed.
Be polite, be on topic, don't ask something that's trivial to answer for yourself, and consider the value of the question to other readers... and you don't have to be already a wizard on the given topic to discuss it.