The Waking Sands is still well-hidden, and honestly, Ul'dah's not exactly the best place for an underground, anti-Garlean organization to be--we have members of the Syndicate who still engage in trade with the Empire as far as I know, and with only money on their minds, rumor or hearsay might give away the fact that they have an anti-Garlean operation going on in the city--not to mention, Lolorito and his Brass Blades aren't exactly the most trustworthy soldiers of the city, and they're in a lot of different places around Ul'dah.
Their hiding place may actually be better than the one in Ul'dah, mainly because the Brass Blade influence isn't as heavy; like you mentioned, the Waking Sands was originally referred to as the Merchant Wards, and, seeing as Minfilia has the power to give the player a license to get a retainer, to any other normal person not involved with the Scions, Minfilia's just running a normal business with the retainers. (The Ashcrown Consortium does the same sort of thing in 1.0 if I'm remembering it right--they're thought of as just a normal business, but very few people know that it's a crystal trade system run entirely by sylphs.) Really, the only reason they were discovered as a secret organization was because
Lahabrea-Thancred sold their location out to Gaius and his tribuni.
In the aftermath of that, they've still decided to stay there and don't seem to want to change it. That may be because most people might think of the Scions as simply a "business" Minfilia runs, but in reality, it's much more than that.
There were probably very few people who realized just how severe the downfall of the Scions post-Titan was--Alphinaud mentions in the scenes after that word has spread of their demise, but the only ones who really get the impact of this are the GC leaders, who are kind of terrified and fear for the worst without them, which is why he mentions the city-states attempting to take as much precautionary action as possible, I think.
Mysteltain is also probably right with the developer's perspective--They most likely didn't want Ul'dah to be the main hub city as it was in 1.0 and then have all the other cities totally deserted. (And it seems to be working, since the GC percentage of the Flames have gone down considerably from 1.0 and now it's pretty balanced.)