The Architecture of Mobile Ad Hoc Network (MANET) is grouped into three main classifications which are :Enabling Technologies, Networking and Middleware and applications.
In general, the nodes of the airborne MANET are connected by much higher bandwidth links than terrestrial MANETs. The airborne nodes also have much greater line-of-sight radio range that increases their possible connections. These characteristics could affect routing algorithm and the transport layer design.
I do not see a reason why their layered architecture would be affected. The mobility and capabilities of nodes will certainly be affected, mainly affecting the details of the physical (PHY) layer. This in turn may affect the applicable algorithms and protocols at the link and network layer. I do not think any higher layers should be affected.