Potentially but avoidably intrusive perceptions vs amazing experiences may result depending upon how opt-in is socialized, how ads are placed, how notifications are issued and the quality of identification management platform, integration SDK /API, sensitivity to personal preference and privacy and experiential relevance given a wide variable of environmental contexts and user modality.
Beacon deployment will increase 1000% in 2015 according to BI. Apps white listed on beacon platforms will issue notifications and launch experiences that may or may not be perceived as relevant or intrusive depending on brand /user dialog and story continuity.
Deep linking is just as possible with NFC, media tags, contactless transaction terminals and products. I've worked on some very successful examples with sports apparel that were diligent in setting and meeting user expectation.
What I'm seeing in the market is mobile proximity connected with programmatic ad placement, RTB, publication, lifestyle and brand apps. There's a through line business case that means revenue for app developers, but like any reward it's not without risk.
Ultimately, apps simply have to be connected to IOT media, cross devices and environments to facilitate user experience and connect mobile attribution with commerce transaction. I would advise you really (really) do your homework on alliance partners and platform, privacy and data use policy, then take the agile test learn and deploy approach.
Hope this is helpful. Look forward to perhaps engaging with you further, and wishing you success!