Nothing to do with spires! This is a technical historical term referring to rammed earth wall construction. The walls they're referring to here are tapias: rammed earth walls (with brick reinforcements in this case), which were extremely common in Spain. They were built using a wooden formwork construction consisting of vertical side boards, known as shutters, with wooden clamps to hold them together. The builders filled in the space between the side boards (shutters) with earth and tamped it down to make the wall, then removed the formwork and moved on to the next section.

http://en.wikipedia.org/wiki/Rammed_earth
http://es.wikipedia.org/wiki/Tapial
http://rammedearthconsulting.com/rammed-earth-formwork.htm

Well now, the agujas are elements of the wooden clamp contraptions that hold the side boards (shutters) in position. Here's a good explanation from Juan de Villanueva in his Arte de albañilería (1827), chapter 5 ("De las tapias de tierra"):

"Para construir tapias de tierra es preciso hacer los cajones con dos tableros que se llaman tapiales (lam. III, fig. 1) [...].
Ármanse y colócanse á los gruesos que se quiere por medio de dos cárceles, ó digamos aros, compuestos cada uno de cuatro piezas, que las dos se llaman agujas (lam. III, fig. 2), y las otras dos costales (Id. fig. 3), y las agujas son algunas veces de hierro. [....] (p. 25)
[...] descúbranse los agujeros de las agujas superiores, donde se colocarán sus clavijas ó clavos, que los mantengan en tanto que se trabaje y macice la tapia (lam. III, fig. 4)." (p. 26)
https://books.google.es/books?id=6v1ytJIyDCUC&pg=PA27-IA1&lp...

You can see what he's talking about by looking at lámina III a couple of pages above this, and comparing it with the photo in my third reference above.

So the agujas are the horizontal members of the square contraptions called "cárceles" that hold the boards in place and resist the lateral pressure as the wall is tamped down. As you pack the earth in it settles round these agujas, and when they're removed they leave holes through the wall.

Horizontal members of this kind are called ties:

"The presence of the putlog holes of the wooden cross ties helps us to reconstruct the process of the wall's construction."
Rammed Earth Conservation, p. 110a
https://books.google.es/books?id=A41rcHptt38C&pg=PA110&lpg=P...


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Note added at 8 hrs (2015-02-26 17:38:01 GMT)
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You might even say "the holes left by the cross ties".

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Note added at 21 hrs (2015-02-27 06:32:43 GMT)
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On reflection, I'd be inclined to follow bigedsenior's suggestion and call them "putlog holes" rather than just "holes"; it would make it clearer what this is about.
http://en.wikipedia.org/wiki/Putlog_hole