That's citizenship by naturalisation, it means your daughter is a citizen (you can pass citizenship on).
So the issue is: Canadian citizens must enter Canada by their Canadian passport (or at least 'as' Canadian citizens). Although your daughter does not have any proof (yet) she is a Canadian citizen, that is separate from her 'acquiring' citizenship (she cannot acquire citizenship - she was born one, just doesn't have the docs).
Put differently: as the daughter of a Canadian-by-naturalisation, she is a presumed citizen. (This is not a legal term, my own phrasing for simplicity)
If she applies for an ETA, she will likely be refused - and it's important that you do not misrepresent / misstate anything on the ETA form. And with a Bosnian passport, she cannot board the flight without the ETA. In other words, she will need Canadian passport to board the flight to Canada.
This is why the proper approach is to apply for her citizenship and for a 'temporary' passport (basically temporary because it is issued in precisely such cases, where the applicant is a presumed citizen but hasn't received the citizenship documentation yet).
Note, I do not know - it may be possible for her to arrive at a land border eg through USA and for you to show the border guards the application for citizenship (i.e. tell them she is a Canadian citizen but hasn\t received the passport yet). At the border, the border guards will let anyone in whom they 'are satisfied is a citizen' into the country (although it's up to you to satisfy them). But it may not be practical for you to travel this way.