I'm using Trigger.io to make an app I can deploy to both the app store and google play. I'm researching baas backends that offer native sdk's for android and apple, but also offer javascript sdk's which I assume are meant for things like Trigger or Phonegap. My question is do the app store guidelines favor one kind of back end service over another? Is javascript risky for backend? I just want to be sure before I pay for a service. The services I'm considering are cloudmine and shephertz.
They shouldn't know anything about your back-end web service.
Sounds like you are talking about making a hybird app though, which is also fine (and is technically a client). There are a ton of hybrid frameworks out there: Ionic, Cordova, Cocoon, PhoneGap, apparently Trigger.io, etc. They wouldn't be useful if app stores rejected them.