As Reported on IGN, Bioshock 3 has been confirmed in the series aswell as a possible Bioshock 4
The wierd bit is they have confirmed it before the 2nd one has already been released...bit of a jump over the gun especially if the sequal to the first game doesn't go as well as the 1st game in the series.
Although nothing is known about the 3rd game in the series it just kinda leaves you knowing that they gonna leave the 2nd game as well on a cliff hanger. So i guess if the 2nd game doesnt go well they could kill this off without many people knowing.
Bioshock 3 - 2011
IGN: BioShock 3