Since the beginning of printed publishing advertisement strategy has been one of the turnkeys together with content strategy. With the huge amount of content flowing from web pages, blind advertisement networks introduced a new strategy, which may not fit completely in the revenue model of digital magazines, or at least not like it could fit on a generic mobile application.
Digital magazines are applications indeed, but there is a bid difference between an application user and a reader. A magazine is a multi part content vehicle which is made of many emotional singularities. Content, Brand, design, media, consistency are just some of the components to which the readers react. Most of the readers feel loyal to their preferred magazine and are willing to subscribe, to be part of a community and with an idea of allegiance.
Advertisement should be part of the components, with highly targeted content and visual impacting experiences. This would positively impact the magazine content itself and create engagement in readers. Have a look at this HTML5 Acura advertisement running on a MagPlus publication.