hi,
I don't see an issue in extending the standard basis risks to be analysed against any other SAP ABAP system.
i Have not had the opportunity to work specifically with EWM, but I have seen cross system risks defined in the past between ECC and SCM systems.
What you may want to consider are identifying and defining any Custom cross system risks that may pose as a SOD risk to the business. I guess you may want to monitor for any potential fraudulent opportunities between activities recorded in the warehouse and the ECC system for good receipts and any changes to delivery details etc.
It is always wise to consider implementing custom risks if you are aware of any such possible suggestions from Audit reports.