Yeah what crazy said. It depends which website you buy it from.
Almost all of them will say something in capital letters or red font, stating which firmware update the flash card is on.
RealHotStuff is pretty good about that. They update the flash cards and when I was buying mine a few weeks ago, I saw in huge red letters- "UPDATED TO NEWEST FIRMWARE - x.xx"
I don't actually remember the number of the firmware, but I checked on my 3ds which I just updated and it was the same one. Then I ordered it and it came 2 days later with the correct firmware.
and plus, even if the website doesn't send you an updated flash card - there is still another method to update the firmware of the flash card even if you have the newest 3ds patch.
I believe it's something along the lines of renaming the update file, starting 3ds, inserting dstwo flash card, waiting for black screen - wait 10 minutes - then restart. and it should be updated.
Also, if you want more current DSTWO info, their offical forums are
http://forum.supercard.sc/forum-26-1.html
All the stuff I posted is just from browsing their forums, this forum and a little documentation from their main website.
It's pretty easy to get the hang of, I mean I only have had a 3ds and the DSTWO for 1-2 weeks and I already got it everything figured out. It's really simple to use.
Hope that helps!