It seemed clear to me but i'll try to simplify it.
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It's like someone with a MAGA hat saying "my secret is I voted for Trump".
That's not a secret, it's obvious.
Nah. It's more like someone wearing red. Then you find out they voted Republican. Then you proclaim how obvious it was all along. Because red states is how they show Republican states on tv.
1. She has black decorative jewels on the shoulders of her armor. 2. She wears a circlet with a black jewel. 3. I don't doubt this decoration is in honor of Shar. 4. Other people wear similar things that aren't in honor of Shar. 5. This is, at the very least, plausible deniability. 6. If you didn't know she worshipped Shar, you wouldn't have guessed. 7. Everyone is Sherlock Holmes in hindsight.
And yes, it's reasonable to expect that someone skilled in actual subterfuge--a real spy for example--would weave a more convincing set of lies. This isn't what we get with Shadowheart. She makes emotional appeals, gives emotional denials, and finally offers an emotional confession. When talking about Raphael, she brags about her knowledge of dark, underhanded psychological tactics, even admitting to a certain admiration. Later, she's on edge when Lae'zel makes a tiefling bow.
The thing is, I don't think we're supposed to see Shadowheart as an effective and devious spy. We're supposed to see her as a character we build sympathy with, as a character we grow to care about, which includes the showing of vulnerability and some amount of "goodness" underneath the mask.
She likes it when we're nice to animals. She's surprised that she grew to care about the tieflings. She's had her memories taken, but she knows she likes night orchids.
When she talks about Shar, she doesn't talk about evil and ransacking villages. She talks about pain, about a pain so great that one can no longer endure, but must rather turn to the darkness, to find peace within.
This is not an evil cleric seeking power from foul gods. This is not even a sophisticated and emotionally mature person. This is a tragedy of a being who we can hope might someday be well again.