There *might* be an argument for your second proposed transcription. 7.6.9 of the updated section 7.6 in the Rules of UEB says "When an opening double quotation mark ⠦ is immediately preceded by a grade 1 indicator, it will be read as a question mark."
However, that same transcription ;(;8./#i) – with two grade 1 symbol indicators within the first three cells of the expression – goes against #5 in BANA's Provisional Guidance on Transcribing Mathematics in UEB, and it just interrupts the flow of the fraction in a way that is unhelpful to the reader.
We believe that ;;(8./#i) is the best transcription of the fraction "question mark over 9." The question mark in the numerator of a fraction is very unlikely to be misread as an opening quotation mark, not least of all because if we did have a quotation mark in that position, we would transcribe the fraction as follows: ;(,7./#i)
So, WE WOULD RECCOMMEND using the first transcription you proposed. ;;(8./#i) A transcriber's note to explain the situation might be in order (e.g., "A question mark is used in the following fraction.").
Thank you for this question!
–Kyle and the whole NBA UEB Tech Material Committee