Will it be useful to add scalar energies to the list of negative influences to be addressed by Soul Matrix Healing (like electromagnetic energies, subconscious programming, etc.)?

In a broader sense this is true, but the ideal solution would perhaps be to make the statement more inclusive by requesting all outside energies intended to work against the client, as this would include many forms of consciousness as well as the carrier energies involved in conveying information as a product of consciousness, whether electromagnetic, scalar, or some other form. After all, this is the intention of your Protocol, to have the broadest possible scope and reach. So this would be our recommendation, to accommodate the issue or opportunity brought forth by this client's prayer request to use it to further the cause of your original intention for the Protocol to make it truly comprehensive.