Interesting Excel Request Training Roster

As you say it is very hard to give definitive answers without more to go on so if you can post an anonymized version of the workbook that could help a lot. That said, I've done a lot with training matrixes and know the feeling. Here are a couple idea that might help:
a) for the 1st issue you could pre-populate all the sheets with generic IDs like EMP#001, EMP#002, .... and then use a lookup to show the name from the 'main' table or blank if not found.
b) for the 2nd issue I would instead recommend adding a column to the 'main' table for active/inactive (or similar) and a matching column on each other table (then use lookup to populate) and then use conditional formatting to 'block' or 'gray' out lines with 'inactive' and/or you can use the table filters on each table to filter those lines out.