Locations that cater mostly to Europeans will have low stock of automatic cars. For this reason I generally rent from airports to be safe. However, Sants is a large transit center. Do you think it's a reasonable bet that rental agencies there probably will have an automatic or should I stick to the airport?
Have a look at each company's website for the location - it should show you the cars available to book. Don't forget that there are an increasing number of hybrids which are, in essence, automatic.
I've been renting in Spain for years--at train stations, in cities, and at airports. I have never had a problem finding an automatic transmission rental.
Just take a look at.the various agencies and what they offer. I rent from SIXT in Spain, and in Italy.
SIXT has 38 choices of automatics at Sants, on random dates I chose in July.