Notepad++ can't display characters like ⊰ http://graphemica.com/%E2%8A%B0 . What is the best settings to solve this problem?
You'd have to ensure that the font you are using for your current Notepad++ theme contains the character in its mapping. For the specific example you cited, that character should display just fine with Cambria Math.
Depending on your use case, you may want to consider defining a custom style theme for Notepad++ to use.