If you are building an Android native application then you can include the jar file as a provided dependency in your gradle file as described here: EMDK for Android Programming Practices - Zebra Technologies Techdocs
You can then detect whether or not the EMDK class exists at runtime with some form of shim, I do something similar in this application here: EnterpriseBarcodePoC/EMDKProxy.java at master · darryncampbell/EnterpriseBarcodePoC · GitHub
Also, make sure you specify that the library is not required in your manifest file:
<uses-library android:name="com.symbol.emdk" android:required="false"/>
I'm not sure how to do it with Xamarin however since I have never tried, I do not think it would be possible because of the way Xamarin components are built into the application.