That appears to be the norm in all of the Spanish ports
I've visited in the Med as well. Even Gibraltar
leaves the entry processing of visiting yachts to the Marinas
. Only in Portugal
did I encounter an immigration officer at check-in at the Marina, and there it was only the larger marinas
(Horta, Ponta Delgada, and Lagos). In Flores, Sao Jorge and Sines the GNR police processed the paper work. In Terceira and Cascais it was done by the marina office.
My guess is with most visiting yachts in Europe
being from EU and Schengen countries there is not a whole lot for immigration and customs to do and to forego the expense of staffing each marina they've transfered the function to the marina office personnel. The result is I've been in Spanish waters for over 6 weeks, but my passport does not show it as it has not been stamped. I'm not sure if this is a good or bad thing.