Would Non-Iconographic apply to logographic languages?

From a mechanical perspective, no, since they're differing systems. If you wanted it to apply I'd consider accounting for it in the cost of Non Iconographic and Dyslexia since they respectively shifted in their impact in the game though.

Realistically I'd argue that there's some fundamental difference between language and symbols because one could argue the same for the English alphabet or entire words, as they are just abstract symbols.

One might say that the iconographic nature of languages like Chinese might mean you can't tell what the Kanji/etc meant (i.e. that certain words were created to visually represent those concepts), which might give penalties for using it broken/understanding difficult or new words as you can no longer intuit meaning by the symbols themselves, but not really impact the abstract language portions.