Hide Entity from Advanced Find
As you know You should be able to handle this through security role, don't provide read permission on that entity to particular user, and it will be hidden for him.
But if you have read privilege on the entity and still you want that entity not to be shown in Advanced find then there is no supported way.
But there is an unsupported way to achieve the same. CRM exposes below Boolean property in EntityMetadata to identify which entity should appear in Advanced Find.
EntityMetadata.IsValidForAdvancedFind Property - Gets or sets whether the entity is will be shown in Advanced Find.
AttributeMetadata.IsValidForAdvancedFind Property - Gets or sets the property that determines whether the attribute appears in Advanced Find.
Try below query to hide Account entity from Advanced Find.
update MetadataSchema.Entity set IsValidForAdvancedFind = 0 where Name = 'account'
update MetadataSchema.Relationship set IsValidForAdvancedFind = 0
where ReferencingEntityId = (select MetadataSchema.Entity.EntityId from MetadataSchema.Entity where Name = 'account')
and IsValidForAdvancedFind = 1
Reset IIS and clear server(and client) cache.
This will hide the entity for all users on the Advanced Find.