I've seen things like ひ・み・つ and お・わ・り written in tategaki in manga all the time. In fact, aside from the occasional use in variety TV captions and sexy emails from a girlfriend, that's the only place I've seen it. Further, as this Wikipedia page notes, 圏点 are used in both tategaki and yokogaki, being placed above the characters in yokogaki, and to the right in tategaki.
I think there is a vocal emphasis with 圏点, but it's different, more of a overall emphasis on the whole word. Or, indeed, phrase, as I've seen it utilized for whole clauses.
Japanese, general discussion on the language