Most of my short stories so far have been published electronically. A few have been both print and ebook, but most are just ebook.
So far my ebook stories are much more likely to net me royalties, but then, that also might be because I stopped submitting to ebook anthologies unless they offered royalties. There are still quite a few anthologies out there that offer one-time payments that I'm not currently pursuing.
One thing that's very nice about epubbing first is that for most of my epublished stories, the only rights I've sold so far are the electronic ones. Of course, this varies from publisher to publisher—some take only the electronic, some take electronic and audio, and some also option the print anthology rights.
The nice thing is, for all those stories where I retain either the exclusive or non-exclusive print anthology rights, I can still sell those rights, even though the story has already been published once electronically.
In essence, I can get paid twice.
There are a number of "Best of" books put out every year which specifically want stories published in the previous year or so. Other anthologies accept new or previously published works. Many of these are in the one-time-payment model, but since they're print and should be getting me in front of new readers (and, most importantly, I've already been paid once!) I don't mind. Many of these are with editors or publishers I would very much like to work with. You never know when someone will have an invitation-only anthology down the line, and you want them to think of you when they do.
Always be very up-front about what rights you have already sold elsewhere. You don't want to mess that up. If you aren't sure, ask your editor.