When I moved to a more wilderness based style of play; where even if you found a dungeon it was likely to be a ruined temple's crypts or catacombs beneath a ruined city or the sewage system of a living city, I lost a lot of the old mega-dungeon tropes and the magic pool type thing was also lost. I ditched a lot of the mega-dungeon tropes in search of verisimilitude too.
I have been thinking about this because I have recently been considering the way I randomly add places to an encounter table when I make them for an area. A typical encounter table in my Garnia campaign for, say, a wooded area might have a goblin patrol, a wild boar, a bear, a human warband hunting goblins, an abandoned wood-cutter's hut, a shrine to a random god, change in weather, etc. Some of those will only be encountered once, thereafter treated as no result. The shrine gets me thinking about those pools, particularly in Garnia with it's Celtic veneer, because pools and springs were often sacred sites to the Celts.
I have to admit I was also inspired by my recent rediscovery of my Talisman game. In Talisman there are several waters that give different, although fixed, effects; one each for Life, Strength and Craft. Of course those are only good for a fixed number of points each too, which differs from most D&D magic pools as I recall.
The Romans even took advantage of the sacred significance and reputed healing powers of Celtic sacred pools, most notably at Aquae Solis (Bath, England); mind you they were pretty fond of baths to start with. Since I already have non-recurring sacred sites popping up in my random encounters in the form of shrines, I figure maybe it might be a good idea to bring back the pools and springs.