Does Notepad++ show all hidden characters?

In Notepad++ I have set "replace tab with 2 spaces".

When coding in Python I copy-pasted some code from the web and it appeared indented correctly. But running the code resulted in indentation errors, which I solved in the end by removing all "visible" spaces at line beginnings and inserting the same amount of spaces again.

Could it be possible that Scintilla based Notepad++ does not show all special characters, but displays them as spaces? Is there a setting to fix this?

Yes, it does. The way to enable this depends on your version of Notepad++. On newer versions you can use:

Menu View → Show Symbol → *Show All Characters`

or

Menu View → Show Symbol → Show White Space and TAB

(Thanks to bers' comment and bkaid's answers below for these updated locations.)

On older versions you can look for:

Menu View → Show all characters

or

Menu View → Show White Space and TAB

In newer versions of Notepad++ (currently 5.9), this option is under:

View->Show Symbol->Show All Characters

or

View->Show Symbol->Show White Space and Tab