Even in software at L3-7 the encoding tech is probably same of course, however protocols L0-2 is very medium dependent. The loss , noise, signal strength patterns all change depending on the medium so does
Even at L4 and above UDP based stacks benefit in wireless compared TCP based transport, if your application can handle it of course. The next gen HTTP is getting designed around UDP in some part to reflect the changing way people access the internet , a lot more traffic is mobile and wireless today so designing around wireless makes sense.
Personally even as app developer who works only with L7(HTTP) and L6 (SDP) I have specifically developed non trivial optimizations, workflows and APIs for mobile clients which were not needed or used by web clients due to different connection parameters of wired/ WiFi as opposed to wireless 2G/3G .
So yes there is lot of difference and most people working at any layer cannot ignore the medium.
But these would apply to both wired and wireless, no?