Aquifer tiles have very high drainage. Think of it as simply taking a gallon of water from one hole and dumping it into another. It should take longer for the water to disperse, but this is still a game. Pumping them into themselves might not make much since, but endlessly flooding from just one square really doesn't either. You are simply using the aquifers properties against itself.
However that comment from Toady did shock me for two reasons 1) Did he truly mean for aquifers to be impenetrable barriers? 2) Is he that out of touch with the game hes creating?
By now there are about 5 methods for piercing an aquifer (Double-slit, pump-stack, cave-in, freezing, cast-obsidian) with a few minor derivatives of each. 6 if you consider punching the aquifer from below and draining it into caverns/off map edge (while you secure it) is a distinct method. It just seems surprising that he wouldn't even be aware of these methods, not like he both designed the aquifers and the mechanics used to defeat them >.>
Personally, I'd go with either double-slit or pump-stack. Cave-ins and freezing (and obsidan) work fine, but they leave giant holes in the ground. They are also hard to use effectively without knowing the full depth of your aquifer. You can only know with certainty that an aquifer is either 1 level or "more levels" Piercing a 1-level aquifer with the cave-in method isn't too bad. However, you have to increase the size of the plug by 2 every layer you go down. You start with a 5x5 hole (which is a 3x3 plug), but it just keeps increasing by 4 from here (2 is the plug and the other 2 is the channeled out ring). For a 6-layer aquifer you are looking at channeling out a 25x25 hole for a single 1x1 staircase... and I've heard of 13 layer ones. This also means channeling out the entire 21x21 underneath the initial plug (and continued channeling over the aquifer until you get through all levels). All the while you risk dumb dorf's channeling out from under one another/getting caught in the cave-in. What I am getting at is that I'd never use this method other than to quicker pierce a shallow aquifer. Also, its kinda gamey that a cave-in of loose sand would automatically destroy the aquifer. The aquifer-tiles just disintegrate from a single layer of sand hitting them... Cave-ins are weird (and lets not forget the magic of magma-pistons)
Freezing is also dangerous and winds up with a smaller hole than the cave-in (unless you live in a permanent freezing biome, then its even smaller). However, you risk the problem of dwarves channeling out from under one another (which is instant death by freezing). It also requires you to know how large the aquifer is beforehand to do properly. Like the cave-in method, it does work very well for 1-layer aquifers if you start work ASAP in the winter. A single layer only needs 16 squares channeled out and 8 walls put up (as well as a constructed staircase) for most biomes. Again though, this is highly dangerous if you misjudge your freezing period and get caught with a half-dug hole by the time the ice thaws. This whole method relies on the idea that water INSTANTLY freezes when it enters an exposed surface tile. However, I don't think its possible to unflag a tile as "surface" once its been exposed. Maybe... casting obsidian over in a layer over it?
Cast Obsidian is rarely used. If you have a volcano, you can just dig down next to the volcano and you can safely bypass the aquifer without any tom-foolery. The aquifer will never be adjacent to the volcano. If you have a magma-vent, its probably the same thing. Never just settled on a magma vent that wasn't in the 2nd cavern layer, though. However, if you want to re-pierce the aquifer (or you were lucky enough to dig-around it before), you can pump the magma into the aquifer. This will allow you to make a much more compact hole, as your walls will be flush against the aquifer-bearing tiles. You'd start at 3x3 and just increase by 2 for every other layer. This is probably the least "gamey" method of piercing the acquifer, but it also depends on how you get the magma to the surface. Most people will use either giant pump stacks powered by hydro-reactors, or impulse ramps (horrendously, unapologetically exploity). Really hard to move large quantities with minecarts without the impulse ramps. On top of everything else you are still dealing with magma... so all the !FUN! That implies. If you have a volcano/vent present, you can just channel a path for the magma to flow... just be sure to have a magma-safe way of cutting off hte flow.
The pump-stack method is much more compact than hte others and works perfectly fine no matter how deep the aquifer is. However, it uses hydro-reactors and infinitely absorbing water back into the aquifer. My main issue is the often used edge-of-map drain. Now, just using the caverns is one thing, but most will dig to the map edge then smooth/carve fortifications and use that. This is a layer of pure stone. You know what is supposed to be in the tile on the other side of those fortifications? More pure stone! More pure stone for MILES! Its one thing for the water to be reabsorbed into the aquifer, but for water to flow into pure stone and magically disappear?
Double-slit still requires you to endlessly pump back into the aquifer, but this really doesn't become silly until you use the last (isolated) aquifer square as a sink. Otherwise you can just imagine the water being dispersed into the other hundreds of tiles. It doesn't require any exploity or gamey behavior beyond that, but is a rather tedious process of constantly unsuspending walls. On the plus side, your pump stack operator might gain some strength out of it >.>
Again though, there is no default way that we are SUPPOSED to pierce aquifers. The games on creator doesn't even know one of the methods used (yet alone all of them), so take your pick. Use whichever you feel is the right balance between "gamey" and "fun" However, keep in mind that you need to use DF-hack's reveal feature (or have already pierced aquifer) to know the aquifer's "more than 1" depth for use in cave in (and freezing). Trying to guess means leaving several abandoned plugs as you restart the process all over again. You can guess around with freezing method, but if you are wrong it'll greatly increase your time (which is often a factor due to spring thaw). I tend to just use double-slit for any multi-level aquifer. If I can confirm its just a single layer, I'll just drop a 4x4 plug (to leave a 2x2 staircase). The 6x6 hole isn't too bad to "repair."