I believe the special characters you are speaking about are not present inside Morrowind standard fonts (Data Files\Fonts\Magic_Cards_Regular.fnt, Data Files\Fonts\Magic_Cards_Regular_0_Lod_A.tex). When you use a WIndows application you are probably seeing another similar .ttf font with the same name (I'm assuming "Magic_Cards") with the extra characters.
Try this: use the MakeMWFonts to generate the Data Files\Fonts\Magic_Cards_16.fnt, Data Files\Fonts\Magic_Cards_16_0_Lod_A.tex from the .ttf,
change in the Morrowind.ini
[Fonts];Font 0=magic_cards_regularFont 0=Magic_Cards_16
and try typing your special chars [] ingame, for instance in in a map note...