I have recently submitted mine and my wife's application together. For her, I have sent a Diploma only (no transcript) from India that of course doesn't say the medium of instruction is English although the certificate itself is in English. Nor have I sent any special letter mentioning this fact.
My personal 'opinion' is that why would a certificate be in English if the instruction was not in English. Doesn't make sense to me. Although CIC can think otherwise and send our application back if they please. In which case, my wife would have to give an exam I guess.
I do not want to make you worried but I have a bachelor degree in engineering from Egypt, and both the transcript and the diploma are in English. Textbooks were in English and exams were in English but the instruction was 70-80% in Arabic. We used English when it comes to symbols, equations, terminology, etc. For your opinion, they issue transcripts and diplomas in English in order to use them internationally. For instance, I used them when I applied to grad school here in Canada.