According to Leon Morris' commentary on John, the pool near the Church of St. Anne is the best candidate because, for one, it was a double pool. Imagine a big rectangle, cut into two. You have four colonnades, one around each side of the big rectangle. Then you have a fifth colonnade in the middle, bisecting the rectangle, with a pool on either side of that bisecting colonnade. This double pool was not in the shape of a pentagon. The BAR article gets into a muddle when it says that this double pool was "five sided," since each of the two pools had four sides. Five colonnades do not necessarily indicate a five-sided pool!
Anyway, Morris says that the excavations below St. Anne showed the existence of five colonnades. I use the word "colonnade" rather than "portico" for clarity, but probably portico is really better, since in a portico (Latin porticus), people hang out in the spaces between or under the columns, and there is a roof on top to provide shade (Greek: stoa).
Morris points out that the 38 years of the paralytic's illness matches the years of Israel's wandering in the wilderness. There are many connections in the NT that one can make with numbers. I wouldn't argue that an allegorical reading necessarily nullifies a literal reading. Morris says that Augustine explained the five porticoes as an allegory of the five books of the Mosaic Law. They cannot save, Jesus can. As you say above, it doesn't follow that there weren't five porticoes, obviously.
A complication, though, comes from the Copper Scroll from Qumran. Morris says that it speaks of Beth Eshdatain, which favors Bethesda as the correct name of the spot. Morris cites the notorious E.J. Vardaman (pilloried by Rene Salm in various publications) for a reference to this pool in the copper scroll. Apparently the form of "pool" is dual, denoting two pools. But then, the gospel account is misleading, if not simply wrong, because it speaks of one big pool, a κολυμβήθρα. If we take John to be locating his story in the pool that is by the Sheep Pool - so as to get our double pool, i.e. Sheep plus Bethesda - then we have the problem that John describes only Bethesda, the healing pool, as having five στοάς, not the complex Sheep Pool/Bethesda.
So my thought at the moment is, does John actually display first-hand knowledge of Jerusalem? Or is he writing his description at second hand? If the latter, a big piece of the argument for 5:2 as early dating evidence is nullified, and we merely have chronological retrojection.
Still, I'm not totally convinced that the pool near St. Anne's is the one in question. Morris says that there is not an active spring there but that remains of water pipes were found, as though the pools were filled periodically from water piped in from the Temple Mount or elsewhere. But it seems that the stirring of the waters recounted in the story better fits a pool that is fed by underground springs that bubble intermittently. I've read of other pools nr. Jerusalem where this happens. For ancient local people to think that the stirring of the waters was miraculous, when in fact the water was piped in from elsewhere, would be to attribute to them more stupidity than I at least find credible. The problem here is that the "stirring of the waters" is part of a disputed section of the text, not in Sinaiticus or Vaticanus and introduced into Alexandrinus by a corrector, and so on.
