I'm pretty sure it
is the result of the typography features selected (assuming that the app does not have some kind of "smart punctuation" option turned on as well). "CY" fonts are not actually different fonts than the ones with the same name without those letters at the end -- they are just a way of selecting non-Unicode Cyrillic encoding for apps that need it, like Appleworks.
It sure looks like a different font to me. I have a bunch of Helvetica fonts, Helvetica, Helvetica CY, Helvetica Neue, and Helvetica-Narrow. They all look a little different from each other.
Neither Courier nor Geneva exhibit the feature for me in TextEdit. But another font which
can do this (as well as smart quotes) is Palatino.
Not for me. The hyphen and en dash look different, but there's no change if I put a hyphen between two numbers, and nothing in the Typography menu has any effect on this.