The missing aleph is probably the font's fault. If you'd use a font with that glyph, it'd be displayed. Could you post a test file so I can try in in the Cybook, where I can easily use almost any font?
As for the overline, as pdurrant says, I don't think it's possible with mobipocket, you'd have to find a different notation there, maybe something like neg(p|q). It sould be possible in ePUB, though.
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