Learn English – Where is the root morpheme in Modern English ambassador, embassy

I would say that my answer about when to italicize loaned words and phrases is also the most appropriate answer to this question:

I think this is a case where authors can decide for themselves where to draw the line. Or, if the writing is for a certain publication, the editors will have a policy for whether a given word should or should not [have diacritics].

(However, that answer got zero votes, so who knows? I still think it is a good answer.)

Various publications will have strict rules about what diacritics are used and when. For example, The New Yorker always uses diaeresis. Each publication seems to have its own rules for bolding, headers, section numbering, hyphenation, capitalization, reference citation, and so on. And there is no definitive format.

I believe that diacritics fall into this category, as evidenced by their generally inconsistent use (though internally consistent within many publications).

It sounds like you've already answered this question for yourself from the etymological point of view.

With regards to modern English, I wouldn't consider the ab- prefix to actually be a productive negative prefix of any kind. In the case of abduct, it's hard to argue that ab- is a negative prefix at all, especially since the stem duct is not obviously related in English to the meaning of abduct. You have to know Latin to make that connection. In the case of abnormal the ab- prefix does attach to an existing word normal, but its meaning here is simple lexical idiosyncracy.

So it is with abortion: I would argue that the stem abort is morphologically simple in English, with the Latinate prefix ab- being an unanalyzable part of the stem from a synchronic point of view. (And most English speakers have never heard of the word ort, and certainly wouldn't connect it in any way to the word abort.)