They don't yet support it and I don't think they will have strong Ionic integration as we haven't talked with them about it.
However, we recently rolled out Ionic Pro which is similar to App Center, but focused 100% on Ionic apps. Adoption so far has been strong despite only being out a few months, and we're investing a lot in the product. Hope you give it a try and we're excited to have some extra validation from App Center!
Interestingly, the new deeper HockeyApp integration recognized that my apps were built with Cordova, but then just shows a "Cordova support coming soon" page for Android and iOS. (The Windows Cordova app was recognized as UWP rather than Cordova. The Windows Electron app I have wasn't recognized at all, but that is unsurprising.)
However, we recently rolled out Ionic Pro which is similar to App Center, but focused 100% on Ionic apps. Adoption so far has been strong despite only being out a few months, and we're investing a lot in the product. Hope you give it a try and we're excited to have some extra validation from App Center!
http://ionicframework.com/products