Shader warnings on the server are safely ignorable, as the server should not be using any graphics features. Unfortunately, these warnings are output by Unity during asset loading and we cannot disable them at this time. (Or, at least, we're not aware of a way to - if you do and are willing to share, please let us know!)
For example, you may see the following in your server console or logs:
WARNING: Shader Unsupported: 'Standard' - All subshaders removed
WARNING: Shader Did you use #pragma only_renderers and omit this platform?
WARNING: Shader If subshaders removal was intentional, you may have forgotten turning Fallback off?
ERROR: Shader Standard shader is not supported on this GPU (none of subshaders/fallbacks are suitable)