"E" will never be clear after "m" and before a vowel sound.

That's the natural pronunciation. The only problem is a click in "hoje".

You can notice the "e" by the sound "iôge" (this "e" sounds rather like "i", but it will definitely not be separated from "o").

Since "ontem" also sounds like having an "i" (onteim), the ending sound is something like "ontenhioje" or "onteinhoge").

And you can deduce it because "ontem hoje" doesn't make sense. And if there were a comma, there would also be a clear rest in pronunciation, "ontem, ... hoje".