I would worry about stagnant water in the piping/tubing running between the holes through the innards of the tub - so I would talk to a Pool and Spa (your Search the List category) / Hot Tub/Jacuzzi dealer about this. I think I would look at cutting/removing the tubing and capping the ports as close to the tub surface as possible in underneath, then epoxy gluing (or tub and tile caulk if you might one day put this back in service) plastic hole plugs over the holes on the inside of the tub to keep water out.
Dealers/manuyfacturer may have replacement plugs designed for taking the ports/jets out and replacing them, because depending on jet/nozzle design and materials might be tough to get a good seal with a plug on the tub side.
I am thinking this sort of plug - available for all common hole sizes in metric and English dimensions:
https://www.amazon.com/White-Plastic-...
Might also be able to use a press-fit barb plug like this, if the jets are wide open for some distance in -
https://www.amazon.com/dp/B003DC8T9Q/...
