Although pantheon-terminal does actually appear to be applying colours to filenames, it is not those defined in
$LS_COLORS. For example
ls should display executable files as bright green (
ex=01;32), though is instead using a barely visible gray.
I understand if the UX designers wish to apply a separate colour scheme in pantheon-terminal to blend better with the rest of the interface, though the colours getting applied now are unworkable. To test yourself view the output of
ls /bin in both a pantheon-terminal and a VT (Ctrl+Alt+F1). In the pantheon-terminal selecting the text with a cursor will show a silhouette of the 'missing' text. Colours are displayed correctly in the VT.