From the Blah-blah-blah...(Wikipedia)

The iota subscript is today considered an obligatory feature in the spelling of Ancient Greek, but its usage is subject to some variation. In some modern editions of classical texts, the historical spelling with a restored full-size adscript 〈ι〉 is preferred. The same is generally true for works dealing with epigraphy, paleography or other philological contexts where adherence to original historical spellings is considered important.

Probably why Adobe includes both styles when they include polytonic Greek --Arno, Minion, Garamond Premier, etc.

Another thing I've run into is authors who insist the Greek circumflex be a tilde, others who insist on the inverted breve. Fonts have been disqualified from consideration because of this.

In the end, it's probably a matter of how large an audience you want to sell to.

Easiest to just skip the academicians & classical Greek. Academicians are notorious for insisting what they want is the only correct, proper way...

For the Modern Suite, I made adscript the default and subscript a Stylistic Set. I don’t recall the precedent; I probably followed Adobe’s practice, and perhaps discussed this issue at Typophile. That would have been c.2007.

March 2007: http://typophile.com/node/32525

There are no subscripts in modern Greek, so it only makes sense to include them together with polytonic Greek (which is a good idea to include in a typeface with Greek if it is intended for books).
In Classical Greek the default is to use the subscript where it should be used (only few cases of αι, ωι, etc. require subscript, most don't). Using adscript instead of subscript is not correct grammatically, it is a hack to overcome the absence of subscripts in a typeface. Conclusion: if you are going to go polytonic include subscript together with all other possible combinations of diacritics.

Thanks to all of you for your comments! I'll go back to work and put all this advice into it.