Tableau can deal with both options, but it might make sense to combine.
How are you creating the hyper file ?
How often does the data change in both (pre-hyper and Excel) sources ?
My preference would be combine if you could, but that depends on your situation.
I am creating it with Tableau Prep. The data is quite static. Is it even possible to combine a hyper extract and excel tables into ANOTHER hyper extract?
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Definitely (I just tried it in Prep), but I would probably add in the Excel data before you create the initial hyper file. Again, just personal preference but there's no need to create a hyper file to join to an Excel file to create the hyper file that you need