Watching Waterworld prompted me to ask what would happen if the opposite happened: an alien device lands at the lowest point in the Pacific, opens a wormhole about a mile wide and drains it.
Googling it turns up some interesting discussions and maps, but most are based on XKCD’s What If using a 10-meter drain taking millenia. How fast are we talking with a mile-wide drain? Would that create a whirlpool?
One of the footnotes in that What If takes you to a comic with the formula. The flow rate is proportional to the area, so a wormhole 80 times larger in diameter would drain water 6400 times faster.
Your link, if I am reading it correctly, seems to suggest that no whirlpools should appear in your case as long as the depth of the drain is at least twice its diameter. So not immediately even with a mile-wide drain.
Ocean drains about halfway and then stops. Wormhole clogged with plastic.
Cool - instead of taking hundreds of thousands of years, it would only take about a century, give or take, and we’d have decades before the giant whirlpool formed.
Plastic won’t be a problem - I’m betting the aliens would have some sort of anti-clogging counter-measure. 
Still Googling stuff on this - wow, the climate would be effed up. Is it reasonable to assume almost all the new landmass is desert?
Eventually, it would have to be so, as removing the Earth’s oceanic water also serves to remove nearly all of our water. This NOAA page indicates that 97% of the planet’s total water supply is in the oceans.
XKCD also has a What if? regarding a 90 degree rotation of Earth’s landmasses. And he can use some models to determine climate change, which can be subtle or significant. So we can also model the effect of new landmasses.
This is probably accurate, sadly.
Marianas Trench-level pressures make a remarkably effective anti-clog countermeasure.
xkcd says “According to my rough calculations, if an aircraft carrier sank and got stuck against the drain, the pressure would easily be enough to fold it up and suck it through. Cooool.”
That is for a 10-m drain. I don’t think anything floating in the ocean is going to clog this drain.
I don’t think a single drain, even in the deepest part of the ocean would drain all of the water. Of course, it probably wouldn’t make that much difference, but I think some water would be left in various ocean basins (depending on what it would do to the climate).
I wonder…what could we do about it if it happened? I was thinking a large reinforced concrete tube, but it would almost certainly be crushed like a soda can putting it in place. Would perhaps be nice to chuck something down at those dirty alien bastards if we could accomplish it though. 
We could try a few loads of old mattresses.
Read the link to the What If article - yes, many small areas are left with water in basins that become stranded as the ocean declines and the Netherlands take over the world.