I have created a model which at some point writes temporary data to an empty table in a geodatabase. After all the geoprocessing is done the final step in the model is deleting all records in that table.
This produces a message "WARNING 000117: Warning empty output generated."
I don't believe there is a way to supress such messages if you are constructing a model in modelbuilder. The tool would not being doing its job if it was not warning you of unusual situations (such as your empty table). If this is truly upsetting you an alternate approach is to keep an empty copy of your table somewhere, delete the entire table that gets filled with data and then copy over the empty table.